6NIN

Rhodobacter sphaeroides bc1 with STIGMATELLIN A

PDB DOI: https://doi.org/10.2210/pdb6NIN/pdb

Classification: OXIDOREDUCTASE/INHIBITOR
Organism(s): Cereibacter sphaeroides 2.4.1
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2018-12-31 Released: 2019-06-19
Deposition Author(s): Xia, D., Zhou, F., Esser, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.280
R-Value Work: 0.249
R-Value Observed: 0.250

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 616.43 kDa
Atom Count: 41,589
Modelled Residue Count: 5,178
Deposited Residue Count: 5,424
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A D [auth E] G [auth K] J [auth O] M [auth S] A, D [auth E], G [auth K], J [auth O], M [auth S], P [auth W]	445	Cereibacter sphaeroides 2.4.1	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for Q3IY10 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IY10 Go to UniProtKB: Q3IY10
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3IY10
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1	B E [auth F] H [auth L] K [auth P] N [auth T] B, E [auth F], H [auth L], K [auth P], N [auth T], Q [auth X]	272	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q3IY11 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IY11 Go to UniProtKB: Q3IY11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3IY11
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase iron-sulfur subunit	C F [auth G] I [auth M] L [auth Q] O [auth U] C, F [auth G], I [auth M], L [auth Q], O [auth U], R [auth Y]	187	Cereibacter sphaeroides 2.4.1	Mutation(s): 1 EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for Q3IY09 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IY09 Go to UniProtKB: Q3IY09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3IY09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain HB [auth X] SDF format, chain LA [auth L] SDF format, chain SA [auth P] SDF format, chain W [auth B] SDF format, chain ZA [auth T] MOL2 format, chain EA [auth F] MOL2 format, chain HB [auth X] MOL2 format, chain LA [auth L] MOL2 format, chain SA [auth P] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth T]	EA [auth F] HB [auth X] LA [auth L] SA [auth P] W [auth B] EA [auth F], HB [auth X], LA [auth L], SA [auth P], W [auth B], ZA [auth T]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain EA [auth F] Focus chain HB [auth X] Focus chain LA [auth L] Focus chain SA [auth P] Focus chain W [auth B] Focus chain ZA [auth T] Interactions & Density Focus chain EA [auth F] Focus chain HB [auth X] Focus chain LA [auth L] Focus chain SA [auth P] Focus chain W [auth B] Focus chain ZA [auth T]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DB [auth W] SDF format, chain EB [auth W] SDF format, chain IA [auth K] SDF format, chain JA [auth K] SDF format, chain PA [auth O] SDF format, chain QA [auth O] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain WA [auth S] SDF format, chain XA [auth S] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DB [auth W] MOL2 format, chain EB [auth W] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth K] MOL2 format, chain PA [auth O] MOL2 format, chain QA [auth O] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain WA [auth S] MOL2 format, chain XA [auth S]	AA [auth E] BA [auth E] DB [auth W] EB [auth W] IA [auth K] AA [auth E], BA [auth E], DB [auth W], EB [auth W], IA [auth K], JA [auth K], PA [auth O], QA [auth O], S [auth A], T [auth A], WA [auth S], XA [auth S]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DB [auth W] Focus chain EB [auth W] Focus chain IA [auth K] Focus chain JA [auth K] Focus chain PA [auth O] Focus chain QA [auth O] Focus chain S [auth A] Focus chain T [auth A] Focus chain WA [auth S] Focus chain XA [auth S] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DB [auth W] Focus chain EB [auth W] Focus chain IA [auth K] Focus chain JA [auth K] Focus chain PA [auth O] Focus chain QA [auth O] Focus chain S [auth A] Focus chain T [auth A] Focus chain WA [auth S] Focus chain XA [auth S]
SMA Query on SMA Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FB [auth W] SDF format, chain KA [auth K] SDF format, chain RA [auth O] SDF format, chain U [auth A] SDF format, chain YA [auth S] MOL2 format, chain CA [auth E] MOL2 format, chain FB [auth W] MOL2 format, chain KA [auth K] MOL2 format, chain RA [auth O] MOL2 format, chain U [auth A] MOL2 format, chain YA [auth S]	CA [auth E] FB [auth W] KA [auth K] RA [auth O] U [auth A] CA [auth E], FB [auth W], KA [auth K], RA [auth O], U [auth A], YA [auth S]	STIGMATELLIN A C₃₀ H₄₂ O₇ UZHDGDDPOPDJGM-WPPYOTIYSA-N		Interactions Focus chain CA [auth E] Focus chain FB [auth W] Focus chain KA [auth K] Focus chain RA [auth O] Focus chain U [auth A] Focus chain YA [auth S] Interactions & Density Focus chain CA [auth E] Focus chain FB [auth W] Focus chain KA [auth K] Focus chain RA [auth O] Focus chain U [auth A] Focus chain YA [auth S]
6PE Query on 6PE Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain GB [auth W] SDF format, chain V [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain GB [auth W] MOL2 format, chain V [auth A]	DA [auth E], GB [auth W], V [auth A]	1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE C₁₇ H₃₃ N O₈ P PELYUHWUVHDSSU-OAHLLOKOSA-M		Interactions Focus chain DA [auth E] Focus chain GB [auth W] Focus chain V [auth A] Interactions & Density Focus chain DA [auth E] Focus chain GB [auth W] Focus chain V [auth A]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain BB [auth T] SDF format, chain FA [auth F] SDF format, chain JB [auth X] SDF format, chain NA [auth L] SDF format, chain TA [auth P] SDF format, chain Y [auth B] MOL2 format, chain BB [auth T] MOL2 format, chain FA [auth F] MOL2 format, chain JB [auth X] MOL2 format, chain NA [auth L] MOL2 format, chain TA [auth P] MOL2 format, chain Y [auth B]	BB [auth T] FA [auth F] JB [auth X] NA [auth L] TA [auth P] BB [auth T], FA [auth F], JB [auth X], NA [auth L], TA [auth P], Y [auth B]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain BB [auth T] Focus chain FA [auth F] Focus chain JB [auth X] Focus chain NA [auth L] Focus chain TA [auth P] Focus chain Y [auth B] Interactions & Density Focus chain BB [auth T] Focus chain FA [auth F] Focus chain JB [auth X] Focus chain NA [auth L] Focus chain TA [auth P] Focus chain Y [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain CB [auth U] SDF format, chain HA [auth G] SDF format, chain KB [auth Y] SDF format, chain OA [auth M] SDF format, chain VA [auth Q] SDF format, chain Z [auth C] MOL2 format, chain CB [auth U] MOL2 format, chain HA [auth G] MOL2 format, chain KB [auth Y] MOL2 format, chain OA [auth M] MOL2 format, chain VA [auth Q] MOL2 format, chain Z [auth C]	CB [auth U] HA [auth G] KB [auth Y] OA [auth M] VA [auth Q] CB [auth U], HA [auth G], KB [auth Y], OA [auth M], VA [auth Q], Z [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CB [auth U] Focus chain HA [auth G] Focus chain KB [auth Y] Focus chain OA [auth M] Focus chain VA [auth Q] Focus chain Z [auth C] Interactions & Density Focus chain CB [auth U] Focus chain HA [auth G] Focus chain KB [auth Y] Focus chain OA [auth M] Focus chain VA [auth Q] Focus chain Z [auth C]
SR Query on SR Download Ideal Coordinates CCD File SDF format, chain AB [auth T] SDF format, chain GA [auth F] SDF format, chain IB [auth X] SDF format, chain MA [auth L] SDF format, chain UA [auth P] SDF format, chain X [auth B] MOL2 format, chain AB [auth T] MOL2 format, chain GA [auth F] MOL2 format, chain IB [auth X] MOL2 format, chain MA [auth L] MOL2 format, chain UA [auth P] MOL2 format, chain X [auth B]	AB [auth T] GA [auth F] IB [auth X] MA [auth L] UA [auth P] AB [auth T], GA [auth F], IB [auth X], MA [auth L], UA [auth P], X [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain AB [auth T] Focus chain GA [auth F] Focus chain IB [auth X] Focus chain MA [auth L] Focus chain UA [auth P] Focus chain X [auth B] Interactions & Density Focus chain AB [auth T] Focus chain GA [auth F] Focus chain IB [auth X] Focus chain MA [auth L] Focus chain UA [auth P] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.280
R-Value Work: 0.249
R-Value Observed: 0.250
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 356.661	α = 90
b = 145.752	β = 104.97
c = 162.223	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Xia, D.

Zhou, F.

Esser, L.

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2019-06-26
Changes: Data collection, Database references
Version 1.2: 2019-08-21
Changes: Data collection, Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary