SMTL ID : 1ihx.1

Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.147, T.149, T.207, G.208, A.209 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.147, A:T.149, 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: SND.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.230 SO4.4: 5 residues within 4Å: Chain B: S.147, T.149, T.207, G.208, A.209 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.147, B:T.149, B:T.149, B:G.208, B:A.209 Water bridges: B:C.148, B:C.148 SO4.5: 3 residues within 4Å: Chain B: T.178, T.180, R.230 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.178, B:T.180, B:T.180 Salt bridges: B:R.230 SO4.7: 5 residues within 4Å: Chain C: S.147, T.149, T.207, G.208, A.209 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.147, C:T.149, C:T.149, C:G.208, C:A.209 Water bridges: C:T.149 SO4.8: 4 residues within 4Å: Chain C: T.178, T.180, R.230 Ligands: SND.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.178, 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 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.147, D:T.149, D:T.207, D:G.208, D:A.209 SO4.11: 4 residues within 4Å: Chain D: T.178, T.180, R.230 Ligands: SND.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.180 Salt bridges: D:R.230

4 x SND: THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

SND.3: 18 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, M.76, S.94, T.95, F.98, S.118, A.119 Ligands: SO4.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.8, A:R.10, A:I.11, A:N.30, A:M.76, A:S.118 Water bridges: A:N.6, A:N.6, A:G.9, A:G.12 pi-Stacking: A:F.33 SND.6: 18 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, T.95, G.96, F.98, S.118, A.119 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:F.8, B:R.10, B:I.11, B:N.30, B:M.76, B:G.96, B:S.118 Water bridges: B:N.6, B:N.6, B:G.9, B:G.12, B:G.96 pi-Stacking: B:F.33 SND.9: 24 residues within 4Å: Chain C: N.6, G.7, 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, H.175, N.312, E.313, Y.316 Ligands: SO4.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.316 Hydrogen bonds: C:R.10, C:I.11, C:N.30, C:F.33, C:M.76, C:N.312 Water bridges: C:G.9, C:G.9, C:A.179 SND.12: 23 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, M.76, S.94, T.95, G.96, F.98, S.118, A.119, C.148, N.312, E.313, Y.316 Ligands: SO4.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.11, D:Y.316 Hydrogen bonds: D:F.8, D:R.10, D:I.11, D:M.76 Water bridges: D:G.9, D:R.13, D:R.13, D:R.13, D:E.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y.Q. et al., Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-07-31

Peptides

GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE

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