SMTL ID : 1szj.1

STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: P.120, S.147, T.207, G.208, A.209 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.147, A:T.150, A:T.207, A:G.208, A:A.209 Water bridges: A:T.149 SO4.2: 4 residues within 4Å: Chain A: T.178, T.180, R.230 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.178, A:T.180 Water bridges: A:A.179, A:T.180 Salt bridges: A:R.230 SO4.4: 6 residues within 4Å: Chain B: P.120, S.147, T.149, T.207, G.208, A.209 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.147, B:S.147, B:G.208, B:A.209 Water bridges: B:S.147, B:T.149 SO4.5: 4 residues within 4Å: Chain B: T.178, T.180, R.230 Ligands: NAD.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.178, B:T.178, B:T.180 Salt bridges: B:R.230 SO4.7: 5 residues within 4Å: Chain C: P.120, S.147, T.207, G.208, A.209 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.147, C:T.207, C:T.207, C:G.208, C:A.209 Water bridges: C:T.150 SO4.8: 4 residues within 4Å: Chain C: T.178, T.180, R.230 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.180 Water bridges: C:A.179, C:T.180 Salt bridges: C:R.230 SO4.10: 6 residues within 4Å: Chain D: P.120, S.147, T.149, T.207, G.208, A.209 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.147, D:S.147, D:T.149, D:T.207, D:G.208, D:A.209 Water bridges: D:S.147 SO4.11: 4 residues within 4Å: Chain D: T.178, T.180, R.230 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.178, D:T.180, D:T.180 Salt bridges: D:R.230

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

NAD.3: 25 residues within 4Å: Chain A: N.6, G.7, F.8, G.9, R.10, I.11, N.30, D.31, P.32, F.33, I.34, E.75, M.76, S.94, T.95, G.96, F.98, S.118, A.119, C.148, A.179, N.312, E.313, Y.316 Ligands: SO4.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.11, A:Y.316 Hydrogen bonds: A:F.8, A:F.8, A:R.10, A:I.11, A:N.30, A:M.76, A:N.312 Water bridges: A:N.6, A:N.6, A:G.9, A:G.12, A:G.96, A:S.118, A:A.179, A:A.179, A:E.313, A:E.313 pi-Stacking: A:F.33 NAD.6: 25 residues within 4Å: Chain B: N.6, G.7, F.8, G.9, R.10, I.11, N.30, D.31, P.32, F.33, I.34, E.75, M.76, S.94, T.95, G.96, F.98, S.118, A.119, C.148, A.179, N.312, E.313, Y.316 Ligands: SO4.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.11, B:Y.316 Hydrogen bonds: B:N.6, B:F.8, B:R.10, B:I.11, B:N.30, B:M.76, B:N.312 Water bridges: B:F.8, B:G.9, B:G.12, B:R.13, B:E.313 NAD.9: 25 residues within 4Å: Chain C: N.6, G.7, F.8, G.9, R.10, I.11, N.30, D.31, P.32, F.33, I.34, E.75, M.76, S.94, T.95, G.96, F.98, S.118, A.119, C.148, A.179, N.312, E.313, Y.316 Ligands: SO4.8 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.11, C:Y.316 Hydrogen bonds: C:F.8, C:F.8, C:R.10, C:I.11, C:N.30, C:M.76, C:N.312 Water bridges: C:N.6, C:N.6, C:G.9, C:G.12, C:G.96, C:S.118, C:A.179, C:A.179 pi-Stacking: C:F.33 NAD.12: 25 residues within 4Å: Chain D: N.6, G.7, F.8, G.9, R.10, I.11, N.30, D.31, P.32, F.33, I.34, E.75, M.76, S.94, T.95, G.96, F.98, S.118, A.119, C.148, A.179, N.312, E.313, Y.316 Ligands: SO4.11 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.11, D:Y.316 Hydrogen bonds: D:N.6, D:F.8, D:R.10, D:I.11, D:N.30, D:M.76, D:N.312 Water bridges: D:F.8, D:G.9, D:G.12, D:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, S.Y. et al., Preliminary crystallographic studies of lobster D-glyceraldehyde-3-phosphate dehydrogenase and the modified enzyme carrying the fluorescent derivative. J.Mol.Biol. (1983)

Release Date

1998-09-16

Peptides

D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
R

C
G

D
R

D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE

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