6DDG

Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-6


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain8082423 3000334 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRibosomal protein L29 (L29p)8094170 3000713 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyTranslational proteins8089152 3000811 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyRibosomal protein L30p/L7e8076281 3001378 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyZn-binding ribosomal proteins8081583 3001320 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyZn-binding ribosomal proteins8075068 3001320 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyL35p-like8083334 3000790 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyRibosomal protein L368083312 3001346 SCOP2B (2022-06-29)
SSCOP2B SuperfamilyRibosomal protein L48094174 3001146 SCOP2B (2022-06-29)
T [auth V]SCOP2B SuperfamilyRibosomal protein L138066059 3001134 SCOP2B (2022-06-29)
U [auth W]SCOP2B Superfamily50S Ribosomal protein L14-like8093892 3000433 SCOP2B (2022-06-29)
V [auth X]SCOP2B SuperfamilyRibosomal proteins L15p and L18e8070555 3001045 SCOP2B (2022-06-29)
W [auth Y]SCOP2B SuperfamilyRibosomal protein L16p/L10e8076041 3000884 SCOP2B (2022-06-29)
X [auth Z]SCOP2B SuperfamilyProkaryotic ribosomal protein L178089022 3000995 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRibosomal protein L208094941 3000563 SCOP2B (2022-06-29)
DSCOP2B Superfamilyl21p-like8094148 3002005 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRibosomal protein L228076726 3001078 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRibosomal proteins S24e L23 and L15e8086046 3000210 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain8082503 3000334 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyRibosomal L27 protein-like8075030 3000539 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF01245e6ddgA1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01245ECOD (1.6)
JPF00830e6ddgJ1 A: few secondary structure elementsX: Ribosomal protein bL28-related (From Homology)H: Ribosomal protein bL28-relatedT: Ribosomal protein L28F: PF00830ECOD (1.6)
KPF00831e6ddgK1 A: alpha bundlesX: Long alpha-hairpinH: Ribosomal protein L29 (L29p) (From Topology)T: Ribosomal protein L29 (L29p)F: PF00831ECOD (1.6)
LPF00297e6ddgL1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: PF00297ECOD (1.6)
MPF00327e6ddgM1 A: a+b two layersX: Ribosomal protein L30p/L7e (From Topology)H: Ribosomal protein L30p/L7e (From Topology)T: Ribosomal protein L30p/L7eF: PF00327ECOD (1.6)
NPF01783e6ddgN1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01783ECOD (1.6)
OPF00471e6ddgO1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF00471ECOD (1.6)
PPF00468e6ddgP1 A: extended segmentsX: 50S ribosomal protein L34 (From Topology)H: 50S ribosomal protein L34 (From Topology)T: 50S ribosomal protein L34F: PF00468ECOD (1.6)
QPF01632e6ddgQ1 A: a+b two layersX: Ribosomal protein L35p (From Topology)H: Ribosomal protein L35p (From Topology)T: Ribosomal protein L35pF: PF01632ECOD (1.6)
RPF00444e6ddgR1 A: few secondary structure elementsX: Ribosomal protein L36 (From Topology)H: Ribosomal protein L36 (From Topology)T: Ribosomal protein L36F: PF00444ECOD (1.6)
SPF00573e6ddgS1 A: a/b three-layered sandwichesX: Ribosomal protein L4 (From Topology)H: Ribosomal protein L4 (From Topology)T: Ribosomal protein L4F: PF00573ECOD (1.6)
BPF00181e6ddgB2 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00181ECOD (1.6)
BPF03947e6ddgB1 A: beta barrelsX: SH3H: SH3T: SH3F: PF03947ECOD (1.6)
T [auth V]PF00572e6ddgV1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L13 and L16-A (From Topology)T: Ribosomal protein L13 and L16-AF: PF00572ECOD (1.6)
U [auth W]PF00238e6ddgW1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: PF00238ECOD (1.6)
V [auth X]PF00828e6ddgX1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal proteins L15p and L18e (From Topology)T: Ribosomal proteins L15p and L18eF: PF00828ECOD (1.6)
W [auth Y]PF00252e6ddgY1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal protein L10eF: PF00252ECOD (1.6)
X [auth Z]PF01196e6ddgZ1 A: a+b two layersX: Enolase-N/ribosomal proteinH: Prokaryotic ribosomal protein L17 (From Topology)T: Prokaryotic ribosomal protein L17F: PF01196ECOD (1.6)
Y [auth a]PF00861e6ddga1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF00861ECOD (1.6)
CPF00453e6ddgC1 A: alpha arraysX: PABP domain-likeH: Ribosomal protein L20 (From Topology)T: Ribosomal protein L20F: PF00453ECOD (1.6)
DPF00829e6ddgD1 A: beta barrelsX: Ribosomal protein L21p (From Topology)H: Ribosomal protein L21p (From Topology)T: Ribosomal protein L21pF: PF00829ECOD (1.6)
EPF00237e6ddgE1 A: a+b two layersX: Enolase-N/ribosomal proteinH: Ribosomal protein L22 (From Topology)T: Ribosomal protein L22F: PF00237ECOD (1.6)
FPF00276e6ddgF1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: PF00276ECOD (1.6)
GPF00467,PF17136e6ddgG1 A: beta barrelsX: SH3H: SH3T: SH3F: PF00467,PF17136ECOD (1.6)
HPF01386e6ddgH1 A: beta barrelsX: Ribosomal protein L25-likeH: Ribosomal protein L25-like (From Topology)T: Ribosomal protein L25-likeF: PF01386ECOD (1.6)
IPF01016e6ddgI1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal L27 proteinF: PF01016ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF01245Ribosomal protein L19 (Ribosomal_L19)Ribosomal protein L19- Family
PF00830Ribosomal L28 family (Ribosomal_L28)Ribosomal L28 family- Family
PF00831Ribosomal L29 protein (Ribosomal_L29)Ribosomal L29 protein- Family
PF00297Ribosomal protein L3 (Ribosomal_L3)Ribosomal protein L3- Family
PF00327Ribosomal protein L30p/L7e (Ribosomal_L30)Ribosomal protein L30p/L7eThis family includes prokaryotic L30 and eukaryotic L7.Domain
PF01783Ribosomal L32p protein family (Ribosomal_L32p)Ribosomal L32p protein family- Family
PF00471Ribosomal protein L33 (Ribosomal_L33)Ribosomal protein L33- Family
PF00468Ribosomal protein L34 (Ribosomal_L34)Ribosomal protein L34- Family
PF01632Ribosomal protein L35 (Ribosomal_L35p)Ribosomal protein L35- Family
PF00444Ribosomal protein L36 (Ribosomal_L36)Ribosomal protein L36- Domain
PF00573Ribosomal protein L4/L1 family (Ribosomal_L4)Ribosomal protein L4/L1 family- Family
PF03947Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C)Ribosomal Proteins L2, C-terminal domain- Domain
PF00181Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2)Ribosomal Proteins L2, RNA binding domain- Domain
T [auth V]PF00572Ribosomal protein L13 (Ribosomal_L13)Ribosomal protein L13- Family
U [auth W]PF00238Ribosomal protein L14p/L23e (Ribosomal_L14)Ribosomal protein L14p/L23e- Domain
V [auth X]PF00828Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A)Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A- Family
W [auth Y]PF00252Ribosomal protein L16p/L10e (Ribosomal_L16)Ribosomal protein L16p/L10e- Domain
X [auth Z]PF01196Ribosomal protein L17 (Ribosomal_L17)Ribosomal protein L17- Family
Y [auth a]PF00861Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (Ribosomal_L18p)Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast- Family
PF00453Ribosomal protein L20 (Ribosomal_L20)Ribosomal protein L20- Family
PF00829Ribosomal prokaryotic L21 protein (Ribosomal_L21p)Ribosomal prokaryotic L21 protein- Family
PF00237Ribosomal protein L22p/L17e (Ribosomal_L22)Ribosomal protein L22p/L17eThis family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.Domain
PF00276Ribosomal protein L23 (Ribosomal_L23)Ribosomal protein L23- Family
PF17136Ribosomal proteins 50S L24/mitochondrial 39S L24 (ribosomal_L24)Ribosomal proteins 50S L24/mitochondrial 39S L24- Family
PF00467KOW motif (KOW)KOW motif- Family
PF01386Ribosomal L25p family (Ribosomal_L25p)Ribosomal L25p familyRibosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress.Domain
PF01016Ribosomal L27 protein (Ribosomal_L27)Ribosomal L27 protein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
50S ribosomal protein L19
50S ribosomal protein L28
50S ribosomal protein L29
50S ribosomal protein L3
50S ribosomal protein L30
50S ribosomal protein L32
50S ribosomal protein L33
50S ribosomal protein L34
50S ribosomal protein L35
50S ribosomal protein L36
50S ribosomal protein L4
50S ribosomal protein L2
T [auth V]50S ribosomal protein L13
U [auth W]50S ribosomal protein L14
V [auth X]50S ribosomal protein L15
W [auth Y]50S ribosomal protein L16
X [auth Z]50S ribosomal protein L17
Y [auth a]50S ribosomal protein L18
Z [auth 1]23S rRNA---
AA [auth 2]5S rRNA---
50S ribosomal protein L20
50S ribosomal protein L21
50S ribosomal protein L22
50S ribosomal protein L23
50S ribosomal protein L24
50S ribosomal protein L25
50S ribosomal protein L27

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR001857Large ribosomal subunit protein bL19Family
IPR038657Large ribosomal subunit protein bL19 superfamilyHomologous Superfamily
IPR018257Large ribosomal subunit protein bL19, conserved siteConserved Site
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR001383Large ribosomal subunit protein bL28, bacterial-typeFamily
IPR037147Large ribosomal subunit protein bL28 superfamilyHomologous Superfamily
IPR026569Large ribosomal subunit protein bL28Family
IPR034704Large ribosomal subunit protein bL28/bL31-like superfamilyHomologous Superfamily
IPR001854Large ribosomal subunit protein uL29Family
IPR036049Large ribosomal subunit protein uL29 superfamilyHomologous Superfamily
IPR019926Large ribosomal subunit protein uL3, conserved siteConserved Site
IPR019927Large ribosomal subunit protein uL3, bacterial/organelle-typeFamily
IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
IPR000597Large ribosomal subunit protein uL3Family
IPR036919Large ribosomal subunit protein uL30, ferredoxin-like fold domain superfamilyHomologous Superfamily
IPR005996Large ribosomal subunit protein uL30, bacterial-typeFamily
IPR016082Large ribosomal subunit protein uL30-like, ferredoxin-like fold domainDomain
IPR002677Large ribosomal subunit protein bL32Family
IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
IPR044957Large ribosomal subunit protein bL32, bacterial typeFamily
IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
IPR038584Large ribosomal subunit protein bL33 superfamilyHomologous Superfamily
IPR001705Large ribosomal subunit protein bL33Family
IPR018264Large ribosomal subunit protein bL33, conserved siteConserved Site
IPR020939Large ribosomal subunit protein bL34, conserved siteConserved Site
IPR000271Large ribosomal subunit protein bL34Family
IPR021137Large ribosomal subunit protein bL35-likeFamily
IPR018265Large ribosomal subunit protein bL35, conserved siteConserved Site
IPR001706Large ribosomal subunit protein bL35Family
IPR037229Large ribosomal subunit protein bL35 superfamilyHomologous Superfamily
IPR000473Large ribosomal subunit protein bL36Family
IPR035977Large ribosomal subunit protein bL36 superfamilyHomologous Superfamily
IPR013005Large ribosomal subunit protein uL4-likeFamily
IPR002136Large ribosomal subunit protein uL4Family
IPR023574Large ribosomal subunit protein uL4 domain superfamilyHomologous Superfamily
IPR022669Large ribosomal subunit protein uL2, C-terminalDomain
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR022671Large ribosomal subunit protein uL2, conserved siteConserved Site
IPR005880Large ribosomal subunit protein uL2, bacterial/organellar-typeFamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR022666Large ribosomal subunit protein uL2, RNA-binding domainDomain
IPR014726Large ribosomal subunit protein uL2, domain 3Homologous Superfamily
IPR002171Large ribosomal subunit protein uL2Family
T [auth V]IPR023563Large ribosomal subunit protein uL13, conserved siteConserved Site
T [auth V]IPR005822Large ribosomal subunit protein uL13Family
T [auth V]IPR036899Large ribosomal subunit protein uL13 superfamilyHomologous Superfamily
T [auth V]IPR005823Large ribosomal subunit protein uL13, bacterial-typeFamily
U [auth W]IPR005745Large ribosomal subunit protein uL14, bacterial-typeFamily
U [auth W]IPR036853Large ribosomal subunit protein uL14 superfamilyHomologous Superfamily
U [auth W]IPR000218Large ribosomal subunit protein uL14Family
U [auth W]IPR019972Large ribosomal subunit protein uL14, conserved siteConserved Site
V [auth X]IPR005749Large ribosomal subunit protein uL15, bacterial-typeFamily
V [auth X]IPR021131Large ribosomal subunit protein uL15/eL18Domain
V [auth X]IPR030878Large ribosomal subunit protein uL15Family
V [auth X]IPR001196Large ribosomal subunit protein uL15, conserved siteConserved Site
V [auth X]IPR036227Large ribosomal subunit protein uL15/eL18 superfamilyHomologous Superfamily
W [auth Y]IPR036920Large ribosomal subunit protein uL16 superfamilyHomologous Superfamily
W [auth Y]IPR020798Large ribosomal subunit protein uL16, conserved siteConserved Site
W [auth Y]IPR000114Large ribosomal subunit protein uL16, bacterial-typeFamily
W [auth Y]IPR016180Large ribosomal subunit protein uL16 domainDomain
W [auth Y]IPR047873Large ribosomal subunit protein uL16Family
X [auth Z]IPR036373Large ribosomal subunit protein bL17 superfamilyHomologous Superfamily
X [auth Z]IPR047859Large ribosomal subunit protein bL17, conserved siteConserved Site
X [auth Z]IPR000456Large ribosomal subunit protein bL17Family
Y [auth a]IPR005484Large ribosomal subunit protein uL18Family
Y [auth a]IPR004389Large ribosomal subunit protein uL18, bacterial-typeFamily
IPR035566Ribosomal protein bL20, C-terminalHomologous Superfamily
IPR005813Large ribosomal subunit protein bL20Family
IPR028909Large ribosomal subunit protein bL21-likeFamily
IPR001787Large ribosomal subunit protein bL21Family
IPR036164Large ribosomal subunit protein bL21-like superfamilyHomologous Superfamily
IPR047867Large ribosomal subunit protein uL22, bacterial/organelle-typeFamily
IPR018260Large ribosomal subunit protein uL22, conserved siteConserved Site
IPR036394Ribosomal protein uL22 superfamilyHomologous Superfamily
IPR001063Large ribosomal subunit protein uL22Family
IPR005727Large ribosomal subunit protein uL22, bacterial/chloroplast-typeFamily
IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
IPR013025Large ribosomal subunit protein uL23-likeFamily
IPR003256Large ribosomal subunit protein uL24Family
IPR041988Large ribosomal subunit protein uL24, KOW domainDomain
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR005824KOWDomain
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR005825Large ribosomal subunit protein uL24, conserved siteConserved Site
IPR011035Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamilyHomologous Superfamily
IPR001021Ribosomal protein bL25, long-formFamily
IPR029751Large ribosomal subunit protein bL25, L25 domainDomain
IPR037121Large ribosomal subunit protein bL25, C-terminalHomologous Superfamily
IPR020057Large ribosomal subunit protein bL25, beta domainDomain
IPR020056Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminalHomologous Superfamily
IPR001684Large ribosomal subunit protein bL27Family
IPR018261Large ribosomal subunit protein bL27, conserved siteConserved Site