SMTL ID : 5c7o.1

Structure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase holo form with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 33 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, G.14, N.32, D.33, P.34, F.35, I.36, C.77, K.78, E.79, S.96, T.97, G.98, V.99, Y.100, L.101, S.120, A.121, S.150, C.151, H.178, T.181, A.182, N.315, E.316, Y.319 Chain C: P.190 Ligands: SO4.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.319 Hydrogen bonds: A:F.10, A:R.12, A:I.13, A:K.78, A:Y.100, A:N.315 Water bridges: A:N.8, A:F.10, A:G.11, A:G.14, A:G.98, A:G.98, A:H.178, A:A.182, A:A.182 pi-Stacking: A:F.35 NAD.3: 33 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, G.14, N.32, D.33, P.34, F.35, I.36, K.78, E.79, P.80, S.96, T.97, G.98, V.99, Y.100, L.101, S.120, A.121, S.150, C.151, H.178, T.181, A.182, N.315, E.316, Y.319 Chain D: P.190 Ligands: SO4.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.319 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:K.78, B:Y.100, B:N.315 Water bridges: B:N.8, B:F.10, B:G.11, B:G.14, B:N.32, B:G.98, B:G.98, B:A.182, B:A.182, B:E.316 pi-Stacking: B:F.35 NAD.5: 33 residues within 4Å: Chain A: P.190 Chain C: N.8, G.9, F.10, G.11, R.12, I.13, G.14, N.32, D.33, P.34, F.35, I.36, C.77, K.78, E.79, S.96, T.97, G.98, V.99, Y.100, L.101, S.120, A.121, S.150, C.151, H.178, T.181, A.182, N.315, E.316, Y.319 Ligands: SO4.6 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.13, C:Y.319 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:K.78, C:Y.100, C:N.315 Water bridges: C:N.8, C:F.10, C:G.11, C:G.14, C:G.98, C:G.98, C:H.178, C:A.182, C:A.182 pi-Stacking: C:F.35 NAD.7: 33 residues within 4Å: Chain B: P.190 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, G.14, N.32, D.33, P.34, F.35, I.36, K.78, E.79, P.80, S.96, T.97, G.98, V.99, Y.100, L.101, S.120, A.121, S.150, C.151, H.178, T.181, A.182, N.315, E.316, Y.319 Ligands: SO4.8 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.13, D:Y.319 Hydrogen bonds: D:F.10, D:R.12, D:I.13, D:K.78, D:Y.100, D:N.315 Water bridges: D:N.8, D:F.10, D:G.11, D:G.14, D:N.32, D:G.98, D:G.98, D:A.182, D:A.182 pi-Stacking: D:F.35

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: T.181, T.183, R.233 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.181, A:T.183 Water bridges: A:T.183, A:T.183, A:R.233 Salt bridges: A:R.233 SO4.4: 5 residues within 4Å: Chain B: T.181, A.182, T.183, R.233 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.181, B:T.183, B:T.183 Water bridges: B:R.233 Salt bridges: B:R.233 SO4.6: 4 residues within 4Å: Chain C: T.181, T.183, R.233 Ligands: NAD.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.181, C:T.183 Water bridges: C:T.183, C:T.183, C:R.233 Salt bridges: C:R.233 SO4.8: 5 residues within 4Å: Chain D: T.181, A.182, T.183, R.233 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.181, D:T.183, D:T.183 Water bridges: D:R.233 Salt bridges: D:R.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Danshina, P.V. et al., Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme. Mol. Hum. Reprod. (2016)

Release Date

2016-03-09

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