SMTL ID : 3h9e.1

Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) complex with NAD and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: N.13, G.14, F.15, G.16, R.17, I.18, N.37, D.38, P.39, F.40, I.41, C.82, K.83, S.101, T.102, G.103, Y.105, S.125, A.126, C.156, A.187, N.320, Y.324 Chain C: P.195 Ligands: PO4.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.18, A:Y.324 Hydrogen bonds: A:F.15, A:F.15, A:R.17, A:I.18, A:K.83, A:Y.105, A:N.320 Water bridges: A:N.13, A:G.16, A:G.19, A:N.37, A:G.103, A:A.187, A:A.187 pi-Stacking: A:F.40 NAD.10: 25 residues within 4Å: Chain B: N.13, G.14, F.15, G.16, R.17, I.18, N.37, D.38, P.39, F.40, I.41, C.82, K.83, S.101, T.102, G.103, Y.105, S.125, A.126, C.156, A.187, N.320, Y.324 Chain D: P.195 Ligands: PO4.11 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.18, B:Y.324 Hydrogen bonds: B:F.15, B:F.15, B:R.17, B:I.18, B:K.83, B:Y.105, B:N.320 Water bridges: B:N.13, B:N.13, B:G.16, B:G.19, B:G.103, B:S.125, B:A.187, B:A.187 pi-Stacking: B:F.40 NAD.21: 25 residues within 4Å: Chain A: P.195 Chain C: N.13, G.14, F.15, G.16, R.17, I.18, N.37, D.38, P.39, F.40, I.41, C.82, K.83, S.101, T.102, G.103, Y.105, S.125, A.126, C.156, A.187, N.320, Y.324 Ligands: PO4.22 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.18, C:Y.324 Hydrogen bonds: C:F.15, C:F.15, C:R.17, C:I.18, C:K.83, C:N.320 Water bridges: C:N.13, C:G.16, C:G.19, C:N.37, C:G.103, C:S.125, C:A.187, C:A.187 pi-Stacking: C:F.40 NAD.30: 25 residues within 4Å: Chain B: P.195 Chain D: N.13, G.14, F.15, G.16, R.17, I.18, N.37, D.38, P.39, F.40, I.41, C.82, K.83, S.101, T.102, G.103, Y.105, S.125, A.126, C.156, A.187, N.320, Y.324 Ligands: PO4.31 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.18, D:Y.324 Hydrogen bonds: D:F.15, D:F.15, D:R.17, D:I.18, D:K.83, D:N.320 Water bridges: D:N.13, D:G.16, D:G.19, D:N.37, D:G.103, D:S.125, D:A.187, D:A.187 pi-Stacking: D:F.40

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

PO4.2: 4 residues within 4Å: Chain A: T.186, T.188, R.238 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.186, A:T.186, A:T.188 Water bridges: A:A.187, A:A.187, A:R.238, A:R.238, A:R.238, A:R.238 Salt bridges: A:R.238 PO4.3: 7 residues within 4Å: Chain A: S.155, C.156, T.157, H.183, T.215, G.216, R.238 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.157, A:T.157, A:T.215, A:G.216, A:R.238 Water bridges: A:C.156, A:C.156, A:H.183, A:S.214, A:S.214 Salt bridges: A:H.183 PO4.11: 4 residues within 4Å: Chain B: T.186, T.188, R.238 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.186, B:T.188 Water bridges: B:A.187, B:A.187, B:R.238, B:R.238, B:R.238 Salt bridges: B:R.238 PO4.12: 6 residues within 4Å: Chain B: S.155, C.156, T.157, H.183, T.215, R.238 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.157, B:T.157, B:T.157, B:T.215, B:R.238 Water bridges: B:C.156, B:C.156, B:H.183 Salt bridges: B:H.183 PO4.22: 4 residues within 4Å: Chain C: T.186, T.188, R.238 Ligands: NAD.21 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.186, C:T.186, C:T.186, C:T.188, C:T.188 Water bridges: C:A.187, C:A.187, C:R.238, C:R.238, C:R.238, C:R.238 Salt bridges: C:R.238 PO4.23: 7 residues within 4Å: Chain C: S.155, C.156, T.157, H.183, T.215, G.216, R.238 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.157, C:T.157, C:G.216, C:R.238 Water bridges: C:C.156, C:C.156, C:H.183, C:S.214, C:S.214 Salt bridges: C:H.183 PO4.31: 4 residues within 4Å: Chain D: T.186, T.188, R.238 Ligands: NAD.30 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.186, D:T.186, D:T.188, D:T.188 Water bridges: D:A.187, D:A.187, D:R.238, D:R.238, D:R.238 Salt bridges: D:R.238 PO4.32: 6 residues within 4Å: Chain D: S.155, C.156, T.157, H.183, T.215, R.238 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.157, D:T.157, D:T.157, D:T.215, D:R.238 Water bridges: D:C.156, D:C.156, D:H.183 Salt bridges: D:H.183

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

EDO.4: 4 residues within 4Å: Chain A: R.197, A.199, W.200 Chain B: E.284 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: P.132, M.133, F.134, N.139, K.223 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: E.176, R.252 Chain B: R.252, L.253, N.308, N.310, F.311 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: G.137, V.138, N.139, E.140, N.141 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Y.259, K.263, E.282, A.301, K.302 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.201, P.212, A.213 Chain B: E.284, K.302 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: F.290, D.293 Chain C: R.58 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: E.284 Chain B: R.197, K.198, A.199, W.200 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: P.132, M.133, N.139, K.223 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: V.138, N.139, E.140, N.141 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: R.58 Chain C: F.290, D.293, H.295 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: Y.259, A.301, K.302, G.304 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: Y.259, K.263, E.282, A.301, K.302 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: P.129, D.130, K.223 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: R.197, A.199, W.200 Chain D: E.284 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain C: P.132, M.133, F.134, N.139, K.223 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: E.176, R.252 Chain D: R.252, L.253, N.308, N.310, F.311 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: G.137, V.138, N.139, E.140, N.141 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain C: Y.259, K.263, E.282, A.301, K.302 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: R.201, P.212, A.213 Chain D: E.284, K.302 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: R.58 Chain D: F.290, D.293 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain C: E.284 Chain D: R.197, K.198, A.199, W.200 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain D: P.132, M.133, N.139, K.223 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain D: V.138, N.139, E.140, N.141 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain A: F.290, D.293, H.295 Chain D: R.58 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain D: Y.259, A.301, K.302, G.304 Ligands: EDO.39 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain D: Y.259, K.263, E.282, A.301, K.302 Ligands: EDO.38 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain D: P.129, D.130, K.223 Ligand excluded by PLIP

Links

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Citation

Chaikuad, A. et al., Structure and kinetic characterization of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase, GAPDS. Biochem.J. (2011)

Release Date

2009-05-26

Peptides

Glyceraldehyde-3-phosphate dehydrogenase, testis-specific: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
O

D
P

Glyceraldehyde-3-phosphate dehydrogenase, testis-specific

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