SMTL ID : 1nqa.1

Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ala Complexed With Nad+ and D-Glyceraldehyde-3-Phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 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, R.98, F.99, S.119, A.120, A.151, T.181, N.182, N.314, Y.318 Chain D: L.189 Ligands: G3H.2 19 PLIP interactions: 19 interactions with chain A 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:G.10, A:G.13, A:G.97, A:S.119, A:N.182, A:N.182, A:N.182, A:N.182 NAD.3: 24 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, P.190 Ligands: G3H.4 21 PLIP interactions: 21 interactions with chain B 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:R.98, B:N.182, B:N.314 Water bridges: B:N.7, B:G.10, B:G.13, B:R.14, B:G.97, B:S.119, B:N.182, B:N.182, B:E.315, B:E.315 NAD.5: 23 residues within 4Å: Chain B: L.189 Chain C: 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: G3H.6 20 PLIP interactions: 19 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:R.98, 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.7: 24 residues within 4Å: Chain A: L.189 Chain D: 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, T.181, N.182, N.314, Y.318 Ligands: G3H.8 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

4 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Non-covalent)

G3H.2: 9 residues within 4Å: Chain A: S.150, A.151, T.152, H.178, T.181, D.183, R.196, R.232 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.151, A:T.152 Water bridges: A:N.182, A:D.183, A:R.196, A:R.196 Salt bridges: A:R.196, A:R.232 G3H.4: 8 residues within 4Å: Chain B: A.151, T.152, H.178, T.181, D.183, R.196, R.232 Ligands: NAD.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.151, B:T.152, B:T.152 Water bridges: B:N.182, B:D.183, B:R.196, B:R.232 Salt bridges: B:R.196, B:R.232 G3H.6: 8 residues within 4Å: Chain C: S.150, A.151, T.152, H.178, T.181, R.196, R.232 Ligands: NAD.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:A.151, C:T.152, C:T.181 Water bridges: C:T.152, C:N.182, C:D.183, C:R.196, C:R.196 Salt bridges: C:R.196, C:R.232 G3H.8: 8 residues within 4Å: Chain D: A.151, T.152, H.178, T.181, D.183, R.196, R.232 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:A.151, D:T.152, D:T.152, D:T.181, D:D.183 Water bridges: D:N.182, D:D.183, D:R.196, D:R.196 Salt bridges: D:R.196, D:R.232

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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