3VAZ | pdb_00003vaz

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group

PDB DOI: https://doi.org/10.2210/pdb3VAZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus subsp. aureus MRSA252
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-12-30 Released: 2013-01-02
Deposition Author(s): Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free:
0.277 (Depositor), 0.260 (DCC)
R-Value Work:
0.202 (Depositor), 0.190 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group

Roychowdhury, A., Mukherjee, S., Dutta, D., Das, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 228.53 kDa
Atom Count: 15,730
Modelled Residue Count: 2,005
Deposited Residue Count: 2,064
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase 1	A [auth P] B [auth R] C [auth O] D [auth Q] E [auth B] A [auth P], B [auth R], C [auth O], D [auth Q], E [auth B], F [auth A]	344	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0 Gene Names: gap, gapA, gapA1, SAR0828 EC: 1.2.1.12
UniProt
Find proteins for Q6GIL8 (Staphylococcus aureus (strain MRSA252)) Explore Q6GIL8 Go to UniProtKB: Q6GIL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6GIL8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain L [auth O] SDF format, chain R [auth A] SDF format, chain G [auth P] SDF format, chain K [auth R] SDF format, chain O [auth Q] SDF format, chain P [auth B] MOL2 format, chain L [auth O] MOL2 format, chain R [auth A] MOL2 format, chain G [auth P] MOL2 format, chain K [auth R] MOL2 format, chain O [auth Q] MOL2 format, chain P [auth B] mmCIF format, chain L [auth O] mmCIF format, chain R [auth A] mmCIF format, chain G [auth P] mmCIF format, chain K [auth R] mmCIF format, chain O [auth Q] mmCIF format, chain P [auth B]	G [auth P] K [auth R] L [auth O] O [auth Q] P [auth B] G [auth P], K [auth R], L [auth O], O [auth Q], P [auth B], R [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth P] Focus chain K [auth R] Focus chain L [auth O] Focus chain O [auth Q] Focus chain P [auth B] Focus chain R [auth A] Interactions & Density Focus chain G [auth P] Focus chain K [auth R] Focus chain L [auth O] Focus chain O [auth Q] Focus chain P [auth B] Focus chain R [auth A]
DGY Query on DGY Download Ideal Coordinates CCD File SDF format, chain N [auth O] SDF format, chain T [auth A] MOL2 format, chain N [auth O] MOL2 format, chain T [auth A] mmCIF format, chain N [auth O] mmCIF format, chain T [auth A]	N [auth O], T [auth A]	(2R)-2,3-DIHYDROXYPROPANOIC ACID C₃ H₆ O₄ RBNPOMFGQQGHHO-UWTATZPHSA-N		Interactions Focus chain N [auth O] Focus chain T [auth A] Interactions & Density Focus chain N [auth O] Focus chain T [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth P] SDF format, chain H [auth P] SDF format, chain J [auth P] SDF format, chain M [auth O] SDF format, chain Q [auth B] SDF format, chain S [auth A] MOL2 format, chain I [auth P] MOL2 format, chain H [auth P] MOL2 format, chain J [auth P] MOL2 format, chain M [auth O] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth A] mmCIF format, chain I [auth P] mmCIF format, chain H [auth P] mmCIF format, chain J [auth P] mmCIF format, chain M [auth O] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth A]	H [auth P] I [auth P] J [auth P] M [auth O] Q [auth B] H [auth P], I [auth P], J [auth P], M [auth O], Q [auth B], S [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth P] Focus chain I [auth P] Focus chain J [auth P] Focus chain M [auth O] Focus chain Q [auth B] Focus chain S [auth A] Interactions & Density Focus chain H [auth P] Focus chain I [auth P] Focus chain J [auth P] Focus chain M [auth O] Focus chain Q [auth B] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.277 (Depositor), 0.260 (DCC)
R-Value Work: 0.202 (Depositor), 0.190 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.389	α = 90
b = 155.389	β = 90
c = 317.849	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-02
Type: Initial release
Version 1.1: 2014-11-12
Changes: Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description