SMTL ID : 8br4.1 (3 other biounits)

Structure of GAPDH from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 22 residues within 4Å: Chain A: G.9, F.10, G.11, R.12, I.13, N.38, D.39, I.40, R.84, E.85, S.103, T.104, G.105, F.107, S.127, A.128, C.158, T.188, Q.189, N.320, E.321, Y.324 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.13, A:I.13, A:Y.324 Hydrogen bonds: A:R.12, A:I.13, A:I.40, A:R.84, A:N.320 NAD.3: 21 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, N.38, D.39, R.84, S.103, T.104, G.105, L.106, S.127, A.128, C.158, T.188, Q.189, N.320, E.321, Y.324 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.324 Hydrogen bonds: B:R.12, B:I.13, B:N.38, B:R.84, B:N.320, B:N.320 NAD.4: 21 residues within 4Å: Chain A: P.197 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, N.38, D.39, R.84, S.103, T.104, G.105, S.127, A.128, C.158, T.188, Q.189, N.320, E.321, Y.324 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.13, C:Y.324 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.38, C:R.84, C:N.320 NAD.5: 19 residues within 4Å: Chain B: P.197 Chain D: G.9, F.10, G.11, R.12, I.13, N.38, D.39, S.103, T.104, G.105, S.127, A.128, C.158, T.188, Q.189, N.320, E.321, Y.324 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.13, D:Y.324 Hydrogen bonds: D:F.10, D:R.12, D:I.13, D:N.320

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: A.47, K.51, V.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.63 EDO.6: 3 residues within 4Å: Chain D: S.44, H.48, L.65 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Structure of GAPDH from Mycobacterium tuberculosis. To Be Published

Release Date

2023-11-01

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glyceraldehyde-3-phosphate dehydrogenase

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