8BR4

Structure of GAPDH from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb8BR4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis
Expression System: Mycobacterium tuberculosis H37Ra
Mutation(s): No

Deposited: 2022-11-22 Released: 2023-11-01
Deposition Author(s): Kumar, A., Karthikeyan, S.
Funding Organization(s): Department of Biotechnology (DBT, India), Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.295
R-Value Work: 0.255
R-Value Observed: 0.257

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of GAPDH from Mycobacterium tuberculosis

Kumar, A., Karthikeyan, S.

To be published.

Macromolecule Content

Total Structure Weight: 617.76 kDa
Atom Count: 38,389
Modelled Residue Count: 5,416
Deposited Residue Count: 5,712
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	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	357	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: gap, MT1480 EC: 1.2.1.12
UniProt
Find proteins for P9WN83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN83 Go to UniProtKB: P9WN83
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WN83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain BA [auth J] SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain EA [auth M] SDF format, chain FA [auth N] SDF format, chain GA [auth O] SDF format, chain HA [auth P] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth P] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth H]	AA [auth I] BA [auth J] CA [auth K] DA [auth L] EA [auth M] AA [auth I], BA [auth J], CA [auth K], DA [auth L], EA [auth M], FA [auth N], GA [auth O], HA [auth P], Q [auth A], S [auth B], T [auth C], U [auth D], W [auth E], X [auth F], Y [auth G], Z [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain V [auth D] MOL2 format, chain R [auth A] MOL2 format, chain V [auth D]	R [auth A], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain V [auth D] Interactions & Density Focus chain R [auth A] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.295
R-Value Work: 0.255
R-Value Observed: 0.257
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.886	α = 90
b = 139.166	β = 108.52
c = 141.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Kumar, A.

Karthikeyan, S.

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/HRD/NBA/37/01/2014
Department of Biotechnology (DBT, India)	India	BT/PR13469/BRB/10/1396/2015
Department of Science & Technology (DST, India)	India	EMR/2016/00/1898

Revision History (Full details and data files)

Version 1.0: 2023-11-01
Type: Initial release

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8BR4

Structure of GAPDH from Mycobacterium tuberculosis

Structure of GAPDH from Mycobacterium tuberculosis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)