SMTL ID : 2vyv.1

Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-3-1-mer

Ligands

14 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 4 residues within 4Å: Chain A: P.128, M.129, N.135, K.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.129, A:N.135 FMT.2: 6 residues within 4Å: Chain A: R.53 Chain B: T.275, F.284, E.287, V.292 Ligands: FMT.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.53, A:R.53, B:E.287 FMT.3: 6 residues within 4Å: Chain A: K.132, G.133, A.134, N.135, F.136, D.137 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.133, A:A.134, A:F.136, A:D.137 Water bridges: A:D.137 FMT.5: 4 residues within 4Å: Chain B: P.128, M.129, N.135, K.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.129, B:N.135 FMT.6: 4 residues within 4Å: Chain A: R.53 Chain B: D.283, N.285, E.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.287 FMT.7: 4 residues within 4Å: Chain B: T.275, E.276, D.277 Ligands: FMT.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.275, B:E.276, B:D.277 Water bridges: B:Y.274 FMT.8: 4 residues within 4Å: Chain B: G.133, A.134, F.136, D.137 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.133, B:A.134, B:F.136, B:D.137 FMT.10: 4 residues within 4Å: Chain C: P.128, M.129, N.135, K.217 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.129, C:N.135 FMT.11: 5 residues within 4Å: Chain C: G.133, A.134, N.135, F.136, D.137 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.133, C:A.134, C:F.136, C:D.137 FMT.14: 3 residues within 4Å: Chain D: P.126, M.127, N.133 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.127, D:N.133 FMT.15: 3 residues within 4Å: Chain C: E.287, V.292 Chain D: R.52 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.287, D:R.52, D:R.52 FMT.16: 6 residues within 4Å: Chain D: P.121, S.149, T.152, G.210, A.211, A.214 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.149, D:T.152 Water bridges: D:S.149, D:T.151, D:G.210, D:G.210 FMT.17: 4 residues within 4Å: Chain D: G.131, E.134, P.267, I.271 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.131, D:E.134 FMT.18: 2 residues within 4Å: Chain D: R.18, H.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.18

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

NAD.4: 21 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, E.77, R.78, A.96, T.97, G.98, L.99, F.100, T.120, C.150, A.181, N.314, Y.318 Chain D: P.189 21 PLIP interactions: 2 interactions with chain D, 19 interactions with chain A Water bridges: D:D.187, D:D.187, A:N.8, A:N.8, A:F.10, A:G.11, A:G.14, A:G.98, A:A.181, A:A.181, A:E.315, A:E.315 Hydrophobic interactions: A:I.13, A:Y.318 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:N.33, A:R.78, A:N.314 NAD.9: 22 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, R.78, A.96, T.97, G.98, L.99, T.120, C.150, A.181, N.314, E.315, Y.318 Chain C: P.189 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.13, B:Y.318 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:N.33, B:R.78, B:T.120, B:N.314 Water bridges: B:G.11, B:G.14, B:G.98, B:T.120, B:A.181, B:A.181, C:D.187 NAD.12: 21 residues within 4Å: Chain B: P.189 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, R.78, A.96, T.97, G.98, L.99, T.120, C.150, A.181, N.314, Y.318 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.13, C:Y.318 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.33, C:R.78, C:N.314 Water bridges: C:N.8, C:N.8, C:F.10, C:G.11, C:G.14, C:T.120, C:T.120, C:A.181, C:T.182, B:D.187 NAD.19: 24 residues within 4Å: Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.31, D.32, P.33, F.34, I.35, C.76, K.77, A.95, T.96, G.97, Y.99, T.119, A.120, C.150, A.181, N.314, Y.318 Ligands: 1GP.13 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.12, D:Y.318 Hydrogen bonds: D:N.7, D:F.9, D:F.9, D:R.11, D:I.12, D:N.31, D:K.77, D:T.119, D:N.314 Water bridges: D:G.10, D:G.13, D:R.14, D:G.97, D:T.119, D:A.181, D:A.181, A:D.187 pi-Stacking: D:F.34

1 x 1GP: SN-GLYCEROL-1-PHOSPHATE(Non-covalent)

1GP.13: 6 residues within 4Å: Chain D: C.150, H.177, T.180, T.182, R.232 Ligands: NAD.19 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.177, D:T.180, D:T.180, D:T.182, D:R.232 Water bridges: D:H.177, D:A.181 Salt bridges: D:R.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frayne, J. et al., Structure of Insoluble Rat Sperm Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) Via Heterotetramer Formation with Escherichia Coli Gapdh Reveals Target for Contraceptive Design. J.Biol.Chem. (2009)

Release Date

2008-08-05

Peptides

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: ABC
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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