SMTL ID : 4o59.1

Co-enzyme Induced Conformational Changes in Bovine Eye Glyceraldehyde 3-Phosphate Dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 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, I.35, E.76, R.77, S.95, T.96, G.97, F.99, S.119, A.120, C.149, A.180, N.313, E.314, Y.317 Chain C: P.188 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.11, A:Y.317 Hydrogen bonds: A:F.8, A:F.8, A:R.10, A:I.11, A:N.31, A:R.77, A:N.313 Water bridges: A:N.6, A:N.6, A:F.8, A:R.13, A:G.97, A:S.119, A:A.180, A:A.180 pi-Stacking: A:F.34 NAD.2: 25 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, I.35, E.76, R.77, S.95, T.96, G.97, F.99, S.119, A.120, C.149, A.180, N.313, E.314, Y.317 Chain D: P.188 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.11, B:I.11, B:Y.317 Hydrogen bonds: B:N.6, B:F.8, B:F.8, B:R.10, B:I.11, B:N.31, B:R.77, B:N.313 Water bridges: B:F.8, B:G.9, B:G.12, B:R.13, B:G.97, B:S.119, B:A.180, B:A.180 pi-Stacking: B:F.34 NAD.3: 25 residues within 4Å: Chain A: P.188 Chain C: N.6, G.7, F.8, G.9, R.10, I.11, N.31, D.32, P.33, F.34, I.35, E.76, R.77, S.95, T.96, G.97, F.99, S.119, A.120, C.149, A.180, N.313, E.314, Y.317 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.11, C:I.11, C:Y.317 Hydrogen bonds: C:N.6, C:F.8, C:F.8, C:R.10, C:I.11, C:N.31, C:R.77, C:N.313 Water bridges: C:G.9, C:G.12, C:R.13, C:G.97, C:S.119, C:A.180, C:A.180, A:D.186 pi-Stacking: C:F.34 NAD.4: 25 residues within 4Å: Chain B: P.188 Chain D: N.6, G.7, F.8, G.9, R.10, I.11, N.31, D.32, P.33, F.34, I.35, E.76, R.77, S.95, T.96, G.97, F.99, S.119, A.120, C.149, A.180, N.313, E.314, Y.317 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.11, D:Y.317 Hydrogen bonds: D:N.6, D:F.8, D:F.8, D:R.10, D:I.11, D:N.31, D:R.77, D:N.313 Water bridges: D:F.8, D:G.9, D:G.12, D:G.97, D:S.119, D:A.180, D:A.180, B:D.186 pi-Stacking: D:F.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baker, B.Y. et al., High-resolution crystal structures of the photoreceptor glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with three and four-bound NAD molecules. Protein Sci. (2014)

Release Date

2014-09-24

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
R

D
Q

Glyceraldehyde-3-phosphate dehydrogenase

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