SMTL ID : 1gd1.1

STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.8 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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.232 Salt bridges: A:R.196, A:R.232 SO4.2: 4 residues within 4Å: Chain A: S.150, T.209, G.210, A.211 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.150, A:T.209, A:G.210 Water bridges: A:S.150, A:T.153, A:T.208, A:T.209 SO4.4: 5 residues within 4Å: Chain B: T.181, D.183, R.196, R.232 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.181 Water bridges: B:N.182, B:R.196, 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.150, B:G.210, B:A.211 Water bridges: B:S.150, B:T.153, B:T.208 SO4.7: 5 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: NAD.9 7 PLIP interactions: 7 interactions with chain C Water bridges: C:N.182, C:D.183, C:R.196, C:R.196, C:R.232 Salt bridges: C:R.196, C:R.232 SO4.8: 4 residues within 4Å: Chain C: S.150, T.209, G.210, A.211 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.150, C:G.210, C:A.211 Water bridges: C:T.153, C:T.153, C:T.208, C:T.209, C:T.209, C:T.209 SO4.10: 5 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: NAD.12 5 PLIP interactions: 5 interactions with chain D Water bridges: D:D.183, D:R.196, D:R.196 Salt bridges: D:R.196, D:R.232 SO4.11: 4 residues within 4Å: Chain D: S.150, T.209, G.210, A.211 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.150, D:T.209, D:G.210, D:A.211 Water bridges: D:S.150, D:T.153, D:T.208, D:T.209

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

NAD.3: 25 residues within 4Å: Chain A: 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, C.151, T.181, N.182, N.314, Y.318 Chain D: L.189 Ligands: SO4.1 19 PLIP interactions: 18 interactions with chain A, 1 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 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, D:L.187 NAD.6: 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, C.151, N.182, N.314, Y.318 Chain C: L.189 Ligands: SO4.4 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.12, B:Y.318 Hydrogen bonds: B:F.9, 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:N.7, B:G.10, B:G.13, B:S.119, B:S.119, B:N.182, B:N.182, B:E.315, B:E.315, C:L.187 NAD.9: 25 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, R.98, F.99, S.119, A.120, C.151, T.181, 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, 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 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, C:E.315, B:L.187 NAD.12: 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, C.151, T.181, N.182, N.314, Y.318 Ligands: SO4.10 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.318 Hydrogen bonds: D:F.9, 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:G.97, D:N.182, D:N.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skarzynski, T. et al., Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 A resolution. J.Mol.Biol. (1987)

Release Date

1988-01-16

Peptides

HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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