SMTL ID : 5ddi.1 (1 other biounit)

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: P.121, S.148, T.208, G.209, A.210 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.148, A:S.148, A:G.209, A:A.210 SO4.2: 4 residues within 4Å: Chain A: T.179, T.181, R.231 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.179, A:T.181 Water bridges: A:R.231, A:R.231 Salt bridges: A:R.231 SO4.4: 4 residues within 4Å: Chain B: S.148, T.208, G.209, A.210 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.148, B:T.208, B:G.209, B:A.210 SO4.5: 4 residues within 4Å: Chain B: T.179, T.181, R.231 Ligands: NAD.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.231 SO4.7: 5 residues within 4Å: Chain C: P.121, S.148, T.208, G.209, A.210 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.148, C:S.148, C:G.209, C:A.210 SO4.8: 4 residues within 4Å: Chain C: T.179, T.181, R.231 Ligands: NAD.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.179, C:T.181 Water bridges: C:R.231, C:R.231 Salt bridges: C:R.231 SO4.10: 4 residues within 4Å: Chain D: S.148, T.208, G.209, A.210 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.148, D:T.208, D:G.209, D:A.210 SO4.11: 4 residues within 4Å: Chain D: T.179, T.181, R.231 Ligands: NAD.12 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.231

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

NAD.3: 21 residues within 4Å: Chain A: N.6, G.7, F.8, G.9, R.10, I.11, N.31, D.32, P.33, F.34, E.76, R.77, S.95, T.96, G.97, S.119, A.120, C.149, N.313, Y.317 Ligands: SO4.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.11, A:Y.317 Hydrogen bonds: A:F.8, A:R.10, A:I.11, A:R.77, A:N.313 Water bridges: A:N.6, A:G.9, A:G.12 pi-Stacking: A:F.34 NAD.6: 21 residues within 4Å: Chain B: N.6, G.7, F.8, G.9, R.10, I.11, N.31, D.32, P.33, F.34, E.76, R.77, S.95, T.96, G.97, S.119, A.120, C.149, N.313, Y.317 Ligands: SO4.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.11, B:Y.317 Hydrogen bonds: B:F.8, B:F.8, B:R.10, B:I.11, B:N.31, B:R.77, B:N.313 NAD.9: 21 residues within 4Å: Chain C: N.6, G.7, F.8, G.9, R.10, I.11, N.31, D.32, P.33, F.34, E.76, R.77, S.95, T.96, G.97, S.119, A.120, C.149, N.313, Y.317 Ligands: SO4.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.11, C:Y.317 Hydrogen bonds: C:F.8, C:R.10, C:I.11, C:R.77, C:N.313 Water bridges: C:N.6, C:G.9, C:G.12 pi-Stacking: C:F.34 NAD.12: 21 residues within 4Å: Chain D: N.6, G.7, F.8, G.9, R.10, I.11, N.31, D.32, P.33, F.34, E.76, R.77, S.95, T.96, G.97, S.119, A.120, C.149, N.313, Y.317 Ligands: SO4.11 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.11, D:Y.317 Hydrogen bonds: D:F.8, D:F.8, D:R.10, D:I.11, D:N.31, D:R.77, D:N.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dimova, M. et al., Novel enhancer binding site found in bacteria and eukaryota but not in archea. To Be Published

Release Date

2016-08-24

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
R

C
P

D
R

Glyceraldehyde-3-phosphate dehydrogenase

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