SMTL ID : 4k9d.1 (1 other biounit)

X-ray crystal structure of a Glyceraldehyde 3-phosphate dehydrogenase from Brugia malayi bound to the co-factor NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: N.17, G.18, F.19, G.20, R.21, I.22, N.42, D.43, P.44, F.45, I.46, S.91, K.92, S.110, T.111, G.112, F.114, S.134, A.135, C.165, A.196, N.329, E.330, Y.333 Chain B: P.204 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.22, A:Y.333 Hydrogen bonds: A:N.17, A:F.19, A:F.19, A:R.21, A:I.22, A:N.42, A:K.92, A:N.329 Water bridges: A:G.20, A:G.23, A:G.112 pi-Stacking: A:F.45 NAD.4: 25 residues within 4Å: Chain A: P.204 Chain B: N.17, G.18, F.19, G.20, R.21, I.22, N.42, D.43, P.44, F.45, I.46, S.91, K.92, S.110, T.111, G.112, F.114, S.134, A.135, C.165, A.196, N.329, E.330, Y.333 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.22, B:Y.333 Hydrogen bonds: B:F.19, B:R.21, B:I.22, B:N.42, B:K.92, B:N.329 Water bridges: B:N.17, B:G.20, B:G.23, B:R.24, B:G.112, B:T.195, B:A.196, A:D.202 pi-Stacking: B:F.45 NAD.5: 22 residues within 4Å: Chain C: N.17, G.18, F.19, G.20, R.21, I.22, N.42, D.43, P.44, F.45, S.91, K.92, S.110, T.111, G.112, S.134, C.165, A.196, N.329, E.330, Y.333 Chain D: P.204 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.22, C:Y.333 Hydrogen bonds: C:N.17, C:F.19, C:R.21, C:I.22, C:N.42, C:K.92, C:N.329 Water bridges: C:F.19, C:G.20, C:G.23, C:R.24 NAD.6: 22 residues within 4Å: Chain C: P.204 Chain D: N.17, G.18, F.19, G.20, R.21, I.22, D.43, P.44, F.45, I.46, K.92, S.110, T.111, G.112, S.134, A.135, C.165, A.196, N.329, E.330, Y.333 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.22, D:Y.333 Hydrogen bonds: D:F.19, D:R.21, D:I.22, D:K.92, D:N.329 Water bridges: D:E.330

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: P.141, M.142, N.148, K.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.142, A:N.148 Water bridges: A:T.151, A:T.151 EDO.3: 4 residues within 4Å: Chain A: R.28, H.61, G.301, Y.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.28, A:R.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fairman, J.W. et al., X-ray crystal structure of a Glyceraldehyde 3-phosphate dehydrogenase from Brugia malayi bound to the co-factor NAD. TO BE PUBLISHED

Release Date

2013-05-01

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
H

Glyceraldehyde-3-phosphate dehydrogenase

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