SMTL ID : 6px2.1 (1 other biounit)

Acropora millepora GAPDH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, L.77, K.78, S.96, T.97, G.98, V.99, F.100, S.120, A.121, C.151, T.181, A.182, N.315, E.316, Y.319 Chain D: P.190 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.319 Hydrogen bonds: A:F.9, A:F.9, A:R.11, A:I.12, A:N.32, A:K.78, A:N.315 Water bridges: A:A.182 pi-Stacking: A:F.35 NAD.3: 22 residues within 4Å: Chain B: N.7, G.8, F.9, G.10, R.11, I.12, D.33, P.34, F.35, I.36, S.96, T.97, G.98, F.100, S.120, A.121, C.151, T.181, A.182, N.315, Y.319 Chain C: P.190 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.319 Hydrogen bonds: B:F.9, B:R.11, B:I.12, B:K.78, B:N.315 pi-Stacking: B:F.35, B:F.35 NAD.5: 24 residues within 4Å: Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, K.78, S.96, T.97, G.98, F.100, S.120, A.121, C.151, T.181, A.182, N.315, E.316, Y.319 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.319 Hydrogen bonds: C:F.9, C:F.9, C:R.11, C:I.12, C:K.78, C:N.315 Water bridges: C:G.10, C:I.12, C:G.13, C:S.96 pi-Stacking: C:F.35 NAD.7: 24 residues within 4Å: Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, L.77, K.78, S.96, T.97, G.98, F.100, S.120, A.121, C.151, A.182, N.315, E.316, Y.319 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.319 Hydrogen bonds: D:F.9, D:F.9, D:R.11, D:I.12, D:N.32, D:K.78, D:N.315 Water bridges: D:F.35, D:E.316

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: S.150, C.151, T.152, H.178, T.210, G.211 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.150, A:S.150, A:T.152, A:T.152, A:T.210, A:G.211, A:R.233 Salt bridges: A:H.178 PO4.4: 7 residues within 4Å: Chain B: S.150, C.151, T.152, H.178, T.210, G.211, R.233 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.150, B:T.152, B:T.152, B:T.210, B:G.211, B:R.233 Salt bridges: B:H.178 PO4.6: 7 residues within 4Å: Chain C: S.150, C.151, T.152, H.178, T.210, G.211, R.233 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.150, C:C.151, C:T.152, C:T.152, C:T.152, C:T.152, C:T.210, C:G.211, C:R.233 Salt bridges: C:H.178 PO4.8: 7 residues within 4Å: Chain D: S.150, C.151, T.152, H.178, T.210, G.211, R.233 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:C.151, D:T.152, D:T.152, D:T.210, D:G.211, D:R.233 Salt bridges: D:H.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez, A.M. et al., Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora. Rsc Adv (2021)

Release Date

2019-12-25

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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