SMTL ID : 3pfw.1

Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) complex with NAD, a binary form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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: GOL.4 14 PLIP interactions: 14 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:N.320 Water bridges: A:N.13, A:G.16, A:G.19, A:N.37, A:G.103 pi-Stacking: A:F.40 NAD.5: 26 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, E.321, Y.324 Chain D: P.195 Ligands: GOL.7 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:N.320 Water bridges: B:N.13, B:F.15, B:G.16, B:G.19, B:R.20, B:G.103, B:S.125, B:E.321, B:E.321 pi-Stacking: B:F.40 NAD.8: 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: GOL.11 16 PLIP interactions: 16 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:Y.105, C:N.320 Water bridges: C:N.13, C:G.16, C:G.19, C:N.37, C:G.103, C:S.125 pi-Stacking: C:F.40 NAD.12: 26 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, E.321, Y.324 Ligands: GOL.14 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain B 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:Y.105, D:N.320 Water bridges: D:N.13, D:F.15, D:G.16, D:G.19, D:G.103, D:S.125, D:E.321, B:D.193 pi-Stacking: D:F.40

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: G.137, V.138, E.140, N.141, K.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.137, A:E.140, A:N.141, A:N.141, A:K.166 GOL.3: 8 residues within 4Å: Chain A: S.155, C.156, T.157, H.183, T.215, A.236, R.238 Ligands: GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.155, A:S.155, A:T.157, A:T.215, A:R.238 Water bridges: A:C.156, A:H.183 GOL.4: 5 residues within 4Å: Chain A: T.186, T.188, R.238 Ligands: NAD.1, GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.186, A:A.187, A:T.188, A:T.188, A:T.188, A:R.238 GOL.6: 6 residues within 4Å: Chain B: C.156, T.157, H.183, T.215, A.236, R.238 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.183, B:R.238 Water bridges: B:G.216 GOL.7: 5 residues within 4Å: Chain B: T.186, A.187, T.188, R.238 Ligands: NAD.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.186, B:A.187, B:T.188, B:R.238, B:R.238 GOL.9: 5 residues within 4Å: Chain C: G.137, V.138, E.140, N.141, K.166 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.137, C:E.140, C:N.141, C:N.141, C:K.166 GOL.10: 8 residues within 4Å: Chain C: S.155, C.156, T.157, H.183, T.215, A.236, R.238 Ligands: GOL.11 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.155, C:S.155, C:T.157, C:T.157, C:R.238 Water bridges: C:C.156, C:H.183, C:T.215 GOL.11: 5 residues within 4Å: Chain C: T.186, T.188, R.238 Ligands: NAD.8, GOL.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.187, C:T.188, C:T.188, C:R.238 GOL.13: 6 residues within 4Å: Chain D: C.156, T.157, H.183, T.215, A.236, R.238 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.183, D:T.215, D:R.238 Water bridges: D:G.216 GOL.14: 5 residues within 4Å: Chain D: T.186, A.187, T.188, R.238 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.187, D:R.238, D:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2010-12-15

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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