3RUN

New strategy to analyze structures of glycopeptide antibiotic-target complexes

PDB DOI: https://doi.org/10.2210/pdb3RUN/pdb

Classification: HYDROLASE/ANTIBIOTIC
Organism(s): Tequatrovirus T4, Amycolatopsis orientalis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-05-05 Released: 2012-06-06
Deposition Author(s): Economou, N.J., Townsend, T.M., Loll, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.180
R-Value Work: 0.147
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 21.22 kDa
Atom Count: 1,835
Modelled Residue Count: 175
Deposited Residue Count: 175
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	168	Tequatrovirus T4	Mutation(s): 3 Gene Names: E EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00720
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VANCOMYCIN	B	7	Amycolatopsis orientalis	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
vancosamine-(1-2)-beta-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G14263HU GlyCosmos: G14263HU

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A]	E [auth A], K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	I [auth A], J [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS Query on CCS	A	L-PEPTIDE LINKING	C₅ H₉ N O₄ S		CYS
OMY Query on OMY	B	L-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		TYR

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000204 Query on PRD_000204	B	Vancomycin	Glycopeptide / Antibiotic		Interactions Focus chain B Interactions & Density Focus chain B

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000204 Query on PRD_000204	C	Vancomycin	Glycopeptide / Antibiotic		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.180
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.44	α = 90
b = 60.44	β = 90
c = 96.83	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Economou, N.J.

Townsend, T.M.

Loll, P.J.

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2013-02-27
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2023-12-06
Changes: Data collection

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Help and Resources

3RUN

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2