SMTL ID : 3dbv.1

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH LEU 33 REPLACED BY THR, THR 34 REPLACED BY GLY, ASP 36 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 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: NAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.181 Water bridges: A:R.196, A:R.196 Salt bridges: A:R.196, A:R.232 SO4.2: 5 residues within 4Å: Chain A: S.150, T.152, T.209, G.210, A.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.150, A:T.209, A:G.210, A:A.211 Water bridges: A:T.152 SO4.4: 4 residues within 4Å: Chain B: T.181, R.196, R.232 Ligands: NAD.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: 5 residues within 4Å: Chain B: S.150, T.152, T.209, G.210, A.211 7 PLIP interactions: 7 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.153, B:T.153 SO4.7: 5 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.181, C:T.181 Salt bridges: C:R.196, C:R.232 SO4.8: 5 residues within 4Å: Chain C: S.150, T.152, T.209, G.210, A.211 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.150, C:S.150, C:T.152, C:T.209, C:G.210, C:A.211 Water bridges: C:T.152 SO4.10: 5 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.181 Salt bridges: D:R.196, D:R.232 SO4.11: 5 residues within 4Å: Chain D: S.150, C.151, T.152, T.209, A.211 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.150, D:T.152, D:T.152 Water bridges: D:R.232

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

NAD.3: 24 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, T.34, E.76, R.77, S.95, T.96, G.97, R.98, S.119, A.120, C.151, T.181, N.182, N.314, E.315, Y.318 Ligands: SO4.1 23 PLIP interactions: 21 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:T.34, A:R.77, A:N.182, A:N.314, A:E.315, A:E.315 Water bridges: A:N.7, A:N.7, A:G.10, A:G.13, A:R.14, A:G.97, A:S.119, A:N.182, D:S.190, D:S.190 NAD.6: 23 residues within 4Å: Chain B: G.8, F.9, G.10, R.11, I.12, N.32, D.33, T.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 Ligands: SO4.4 19 PLIP interactions: 19 interactions with chain B 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:T.34, B:R.77, B:N.182, B:N.314 Water bridges: B:N.7, B:N.7, B:G.10, B:G.10, B:G.13, B:R.14, B:N.182, B:N.182 NAD.9: 21 residues within 4Å: Chain C: G.8, F.9, G.10, R.11, I.12, D.33, T.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, Y.318 Ligands: SO4.7 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.12 Hydrogen bonds: C:F.9, C:R.11, C:I.12, C:T.34, C:R.77, C:N.182, C:N.314 Water bridges: C:N.7, C:N.7, C:G.10, C:G.13, C:R.14, C:G.97, C:G.97, C:N.182, C:N.182, C:E.315, B:S.190 pi-Stacking: C:Y.318 NAD.12: 20 residues within 4Å: Chain D: G.8, F.9, G.10, R.11, I.12, N.32, D.33, T.34, R.77, S.95, T.96, G.97, S.119, A.120, C.151, T.181, N.182, N.314, Y.318 Ligands: SO4.10 22 PLIP interactions: 21 interactions with chain D, 1 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:T.34, D:R.77, D:N.182, D:N.314 Water bridges: D:N.7, D:F.9, D:G.10, D:G.13, D:G.97, D:S.119, D:N.182, D:E.315, D:E.315, D:E.315, A:D.188

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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