SMTL ID : 2dbv.1

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.181, D.183, R.196, R.232 Ligands: NDP.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.181, A:T.181, A:R.196 Water bridges: A:R.196 Salt bridges: A:R.232 SO4.2: 5 residues within 4Å: Chain A: S.150, T.152, T.209, G.210, A.211 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.150, A:T.152, A:G.210 Water bridges: A:S.150, A:S.150, A:T.209 SO4.4: 5 residues within 4Å: Chain B: T.181, D.183, R.196, R.232 Ligands: NDP.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.181 Water bridges: B:R.196, B:R.232 Salt bridges: B:R.196, B:R.232 SO4.5: 4 residues within 4Å: Chain B: S.150, T.209, G.210, A.211 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.150, B:T.209, B:T.209, B:G.210, B:A.211 Water bridges: B:T.152, B:T.153, B:R.232 SO4.7: 5 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: NDP.9 4 PLIP interactions: 4 interactions with chain C Water bridges: C:T.181, C:R.196 Salt bridges: C:R.196, C:R.232 SO4.8: 4 residues within 4Å: Chain C: S.150, T.209, G.210, A.211 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.150, C:T.209, C:G.210, C:A.211 Water bridges: C:S.150, C:G.210 SO4.10: 5 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: NDP.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.181 Water bridges: D:N.182, D:D.183, D:R.196, D:R.232 Salt bridges: D:R.196, D:R.232 SO4.11: 5 residues within 4Å: Chain D: S.150, T.208, T.209, G.210, A.211 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.150, D:S.150, D:G.210, D:A.211 Water bridges: D:R.232, D:R.232

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.3: 23 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, G.33, L.34, R.77, S.95, T.96, G.97, S.119, A.120, C.151, T.181, N.182, N.314, E.315, Y.318 Chain D: S.190 Ligands: SO4.1 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.12, A:I.12, A:Y.318 Hydrogen bonds: A:F.9, A:R.11, A:I.12, A:N.32, A:R.77, A:N.182, A:N.314, D:S.190, D:S.190 Water bridges: A:F.9, A:G.10, A:G.13, A:R.14, A:R.14, A:L.34, A:L.34, A:L.34, A:G.97, A:S.119, A:N.182, A:E.315, A:E.315 NDP.6: 24 residues within 4Å: Chain B: G.8, F.9, G.10, R.11, I.12, N.32, G.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, C.151, N.182, N.314, E.315, Y.318 Chain C: S.190 Ligands: SO4.4 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.12, B:I.12, B:Y.318 Hydrogen bonds: B:F.9, B:R.11, B:I.12, B:N.32, B:R.77, B:N.182, B:N.314, C:S.190 Water bridges: B:N.7, B:N.7, B:G.10, B:G.13, B:R.14, B:R.14, B:L.34, B:N.182, B:N.182, C:S.190, C:S.190 NDP.9: 23 residues within 4Å: Chain B: S.190 Chain C: G.8, F.9, G.10, R.11, I.12, N.32, G.33, L.34, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, C.151, T.181, N.182, N.314, Y.318 Ligands: SO4.7 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.12, C:I.12, C:Y.318 Hydrogen bonds: C:F.9, C:R.11, C:I.12, C:N.32, C:R.77, C:N.182, C:N.314, B:S.190 Water bridges: C:N.7, C:G.10, C:G.13, C:G.97, C:S.119, C:N.182, C:N.182, C:N.182, B:S.190, B:S.190 NDP.12: 22 residues within 4Å: Chain A: S.190 Chain D: G.8, F.9, G.10, R.11, I.12, N.32, G.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, S.119, A.120, C.151, N.182, N.314, Y.318 Ligands: SO4.10 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.12, D:I.12, D:Y.318 Hydrogen bonds: D:F.9, D:R.11, D:I.12, D:N.32, D:R.77, D:N.182, D:N.314, A:S.190, A:S.190, A:S.190 Water bridges: D:N.7, D:G.10, D:G.13, D:R.14, D:R.14, D:L.34, D:G.97, D:N.182, D:N.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Didierjean, C. et al., A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+. J.Mol.Biol. (1997)

Release Date

1997-07-07

Peptides

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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