SMTL ID : 1hdg.1

THE CRYSTAL STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA AT 2.5 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: T.181, D.183, R.196, R.232 Ligands: SO4.2, NAD.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.181 Water bridges: A:N.182, A:R.196, A:R.232 Salt bridges: A:R.196, A:R.232 SO4.2: 7 residues within 4Å: Chain A: S.150, C.151, T.152, H.178, T.209, G.210 Ligands: SO4.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.150, A:S.150, A:T.152, A:T.152, A:G.210 Water bridges: A:C.151, A:C.151, A:R.232, A:R.232, A:R.232, A:R.232 Salt bridges: A:H.178 SO4.4: 5 residues within 4Å: Chain B: T.181, D.183, R.196, R.232 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain B Water bridges: B:T.181, B:R.196, B:R.232 Salt bridges: B:R.196, B:R.232 SO4.5: 6 residues within 4Å: Chain B: S.150, C.151, T.152, H.178, T.209, G.210 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.150, B:S.150, B:T.152, B:T.152, B:T.209, B:G.210 Water bridges: B:C.151, B:C.151, B:R.232, B:R.232, B:R.232, B:R.232 Salt bridges: B:H.178 SO4.7: 6 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: SO4.8, NAD.9 5 PLIP interactions: 5 interactions with chain C Water bridges: C:N.182, C:R.196, C:R.232 Salt bridges: C:R.196, C:R.232 SO4.8: 7 residues within 4Å: Chain C: S.150, C.151, T.152, H.178, T.209, G.210 Ligands: SO4.7 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.150, C:S.150, C:T.152, C:T.152, C:T.209, C:G.210 Water bridges: C:C.151, C:C.151, C:R.232, C:R.232, C:R.232, C:R.232 Salt bridges: C:H.178 SO4.10: 5 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: NAD.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.181 Water bridges: D:D.183, D:D.183, D:R.196, D:R.196 Salt bridges: D:R.196, D:R.232 SO4.11: 6 residues within 4Å: Chain D: S.150, C.151, T.152, H.178, T.209, G.210 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.150, D:S.150, D:T.152, D:T.152, D:G.210 Water bridges: D:C.151, D:C.151, D:R.232, D:R.232, D:R.232, D:R.232 Salt bridges: D:H.178

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

NAD.3: 23 residues within 4Å: Chain A: N.6, G.7, F.8, G.9, R.10, I.11, N.33, D.34, L.35, P.78, S.96, T.97, G.98, F.100, T.120, A.121, C.151, N.182, N.314, E.315, Y.318 Chain D: L.189 Ligands: SO4.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.11, A:I.11, A:Y.318 Hydrogen bonds: A:F.8, A:R.10, A:I.11, A:N.33, A:P.78, A:N.182, A:N.314 Water bridges: A:N.6, A:N.6, A:G.9, A:G.12, A:G.98, A:R.101, A:R.101, A:T.120, A:N.182, A:N.182, A:N.182 NAD.6: 21 residues within 4Å: Chain B: G.7, F.8, G.9, R.10, I.11, N.33, D.34, L.35, P.78, S.96, T.97, G.98, F.100, T.120, A.121, C.151, N.182, N.314, Y.318 Chain C: L.189 Ligands: SO4.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.11, B:Y.318 Hydrogen bonds: B:F.8, B:R.10, B:I.11, B:N.33, B:P.78, B:N.182, B:N.314 Water bridges: B:N.6, B:G.9, B:G.12, B:G.98, B:T.120, B:N.182, B:N.182 NAD.9: 23 residues within 4Å: Chain B: L.189 Chain C: N.6, G.7, F.8, G.9, R.10, I.11, N.33, D.34, L.35, P.78, S.96, T.97, G.98, F.100, T.120, A.121, C.151, N.182, N.314, E.315, Y.318 Ligands: SO4.7 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:I.11, C:I.11, C:Y.318 Hydrogen bonds: C:F.8, C:R.10, C:I.11, C:N.33, C:P.78, C:T.120, C:N.182, C:N.314 Water bridges: C:N.6, C:N.6, C:G.9, C:G.12, C:G.98, C:R.101, C:R.101, C:T.120, C:N.182, C:N.182, C:N.182 NAD.12: 21 residues within 4Å: Chain A: L.189 Chain D: G.7, F.8, G.9, R.10, I.11, N.33, D.34, L.35, P.78, S.96, T.97, G.98, F.100, T.120, A.121, C.151, N.182, N.314, Y.318 Ligands: SO4.10 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.11, D:Y.318 Hydrogen bonds: D:F.8, D:R.10, D:I.11, D:N.33, D:P.78, D:T.120, D:N.182, D:N.314 Water bridges: D:N.6, D:G.9, D:G.12, D:G.98, D:T.120, D:N.182, D:N.182, D:E.315, D:E.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korndorfer, I. et al., The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 A resolution. J.Mol.Biol. (1995)

Release Date

1995-03-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
Q

C
O

D
Q

HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE