SMTL ID : 1npt.1

Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 replaced by Ala complexed with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-tetramer

Ligands

4 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.2 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.183, A:R.196, A:R.196 Salt bridges: A:R.196, A:R.232 SO4.3: 5 residues within 4Å: Chain B: T.181, D.183, R.196, R.232 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.183 Water bridges: B:N.182, B:R.196, B:R.196 Salt bridges: B:R.196, B:R.232 SO4.5: 5 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.181 Water bridges: C:R.196, C:R.232 Salt bridges: C:R.196, C:R.232 SO4.7: 5 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: NAD.8 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

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

NAD.2: 22 residues within 4Å: Chain A: G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, F.99, S.119, A.120, A.151, N.182, N.314, Y.318 Chain D: L.189 Ligands: SO4.1 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.12, A:A.151, 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 Water bridges: A:N.7, A:N.7, A:G.10, A:G.13, A:G.97, A:S.119, A:N.182, A:N.182, A:N.182, D:L.187 NAD.4: 23 residues within 4Å: Chain B: G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, A.151, N.182, N.314, Y.318 Chain C: L.189 Ligands: SO4.3 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.12, B:A.151, 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 Water bridges: B:N.7, B:G.10, B:G.13, B:R.77, B:R.77, B:G.97, B:S.119, B:N.182, B:N.182, B:N.182, B:E.315, B:E.315, C:L.187 NAD.6: 23 residues within 4Å: Chain B: L.189 Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, F.99, S.119, A.120, A.151, N.182, N.314, Y.318 Ligands: SO4.5 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.12, C:A.151, 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 Water bridges: C:N.7, C:N.7, C:G.10, C:G.13, C:G.97, C:S.119, C:N.182, C:N.182, B:L.187 NAD.8: 24 residues within 4Å: Chain A: L.189 Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, L.34, E.76, R.77, S.95, T.96, G.97, R.98, F.99, S.119, A.120, A.151, N.182, N.314, Y.318 Ligands: SO4.7 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.12, D:A.151, 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 Water bridges: D:N.7, D:N.7, D:G.10, D:G.13, D:G.97, D:S.119, D:N.182, D:N.182, D:E.315, D:E.315, A:L.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Didierjean, C. et al., Crystal structure of two ternary complexes of phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus stearothermophilus with NAD and D-Glyceraldehyde-3-Phosphate. J.Biol.Chem. (2003)

Release Date

2003-04-22

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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