SMTL ID : 1dss.1

STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: S.147, C.148, T.149, H.175, T.207, G.208, A.209 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.147, A:T.149, A:T.149, A:T.149, A:G.208, A:A.209 Water bridges: A:S.206, A:R.230, A:R.230, A:R.230, A:R.230 Salt bridges: A:H.175 SO4.2: 5 residues within 4Å: Chain A: C.148, T.178, T.180, R.230 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.178, A:T.180, A:T.180 Water bridges: A:A.179, A:A.179, A:R.230, A:R.230 Salt bridges: A:R.230 SO4.4: 6 residues within 4Å: Chain B: S.147, C.148, T.149, H.175, T.207, G.208 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.147, B:T.149, B:T.149, B:T.149, B:G.208 Water bridges: B:R.230, B:R.230, B:R.230, B:R.230 Salt bridges: B:H.175 SO4.5: 5 residues within 4Å: Chain B: C.148, T.178, T.180, R.230 Ligands: NAD.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.178, B:T.178, B:T.180 Water bridges: B:A.179, B:A.179, B:R.230, B:R.230 Salt bridges: B:R.230 SO4.7: 7 residues within 4Å: Chain C: S.147, C.148, T.149, H.175, T.207, G.208, A.209 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.147, C:T.149, C:T.149, C:T.149, C:T.207, C:G.208, C:A.209 Water bridges: C:S.206, C:R.230, C:R.230, C:R.230, C:R.230 Salt bridges: C:H.175 SO4.8: 5 residues within 4Å: Chain C: C.148, T.178, T.180, R.230 Ligands: NAD.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.180, C:T.180, C:T.180 Water bridges: C:A.179, C:A.179, C:R.230, C:R.230 Salt bridges: C:R.230 SO4.10: 6 residues within 4Å: Chain D: S.147, C.148, T.149, H.175, T.207, G.208 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.147, D:T.149, D:T.149, D:T.149, D:T.207, D:G.208 Water bridges: D:R.230, D:R.230, D:R.230, D:R.230 Salt bridges: D:H.175 SO4.11: 5 residues within 4Å: Chain D: C.148, T.178, T.180, R.230 Ligands: NAD.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.178, D:T.180 Water bridges: D:A.179, D:A.179, D:R.230, D:R.230 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 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.11, A:I.11, A:Y.316 Hydrogen bonds: A:N.6, A:F.8, A:F.8, A:R.10, A:I.11, A:N.30, A:M.76, A:N.312 Water bridges: A:G.9, A:G.12, A:R.13, 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 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.11, B:I.11, B:Y.316 Hydrogen bonds: B:N.6, B:F.8, B:F.8, B:R.10, B:I.11, B:N.30, B:M.76, B:N.312 Water bridges: B:G.9, B:G.12, B:G.96, B:G.96, B:A.179, B:A.179, B:E.313, B:E.313 pi-Stacking: B:F.33 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 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.11, C:I.11, C:Y.316 Hydrogen bonds: C:N.6, C:F.8, C:F.8, C:R.10, C:I.11, C:N.30, C:M.76, C:N.312 Water bridges: C:G.9, C:G.12, C:R.13, 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 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.11, D:I.11, D:Y.316 Hydrogen bonds: D:N.6, D:F.8, D:F.8, D:R.10, D:I.11, D:N.30, D:M.76, D:N.312 Water bridges: D:G.9, D:G.12, D:R.13, D:G.96, D:G.96, D:A.179, D:A.179 pi-Stacking: D:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, S.Y. et al., Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor. J.Mol.Biol. (1999)

Release Date

1998-12-09

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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