SMTL ID : 8jb1.1

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 in complex with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 18 residues within 4Å: Chain A: G.129, F.130, G.131, R.132, I.133, R.159, R.169, N.228, T.229, G.230, R.231, T.253, A.254, C.284, N.448, E.449, Y.452 Chain C: N.322 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.133, A:Y.452, A:Y.452 Hydrogen bonds: A:F.130, A:F.130, A:R.132, A:I.133, A:R.231, A:T.253, A:N.448, A:N.448, C:N.322 Water bridges: A:R.159, A:R.169, A:N.315, C:N.322 Salt bridges: A:R.159, A:R.169 pi-Cation interactions: A:R.159, A:R.159 NAP.3: 19 residues within 4Å: Chain B: G.129, F.130, G.131, R.132, I.133, R.159, R.169, N.228, T.229, G.230, R.231, T.253, A.254, C.284, T.314, N.448, Y.452 Chain D: N.322, F.323 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.133, B:Y.452, B:Y.452 Hydrogen bonds: B:F.130, B:F.130, B:R.132, B:I.133, B:R.231, B:N.448, B:N.448, D:N.322 Water bridges: B:R.135, B:R.159, B:R.159, B:R.159, B:R.159, B:E.449, D:F.323 Salt bridges: B:R.159, B:R.169 pi-Cation interactions: B:R.159, B:R.159 NAP.6: 18 residues within 4Å: Chain A: N.322 Chain C: G.129, F.130, G.131, R.132, I.133, R.159, R.169, N.228, T.229, G.230, R.231, T.253, A.254, C.284, N.448, E.449, Y.452 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.133, C:Y.452, C:Y.452 Hydrogen bonds: C:F.130, C:F.130, C:R.132, C:I.133, C:R.231, C:N.448, C:N.448, A:N.322 Water bridges: C:R.159, C:R.169, C:N.315, A:N.322 Salt bridges: C:R.159, C:R.169 pi-Cation interactions: C:R.159, C:R.159 NAP.8: 19 residues within 4Å: Chain B: N.322, F.323 Chain D: G.129, F.130, G.131, R.132, I.133, R.159, R.169, N.228, T.229, G.230, R.231, T.253, A.254, C.284, T.314, N.448, Y.452 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.133, D:Y.452, D:Y.452 Hydrogen bonds: D:F.130, D:F.130, D:R.132, D:I.133, D:R.231, D:T.253, D:N.448, D:N.448, B:N.322 Water bridges: D:R.135, D:R.159, D:R.159, D:R.159, D:R.159, D:T.314, B:F.323 Salt bridges: D:R.159, D:R.169 pi-Cation interactions: D:R.159, D:R.159

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.139, H.179, V.420, G.421, F.450 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.139, A:H.179 Water bridges: A:R.139 GOL.4: 5 residues within 4Å: Chain B: R.139, H.179, V.420, G.421, F.450 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.139, B:H.179 GOL.5: 7 residues within 4Å: Chain B: S.283, C.284, T.285, T.309, H.311, T.342, G.343 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.283, B:T.285, B:T.342, B:G.343 GOL.7: 5 residues within 4Å: Chain C: R.139, H.179, V.420, G.421, F.450 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.139, C:H.179 Water bridges: C:R.139 GOL.9: 5 residues within 4Å: Chain D: R.139, H.179, V.420, G.421, F.450 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.139 GOL.10: 7 residues within 4Å: Chain D: S.283, C.284, T.285, T.309, H.311, T.342, G.343 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.283, D:T.285, D:T.285, D:G.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Son, H.F. et al., Structure-based functional analysis of a novel NADPH-producing glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum. Int.J.Biol.Macromol. (2023)

Release Date

2023-12-06

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glyceraldehyde-3-phosphate dehydrogenase