SMTL ID : 4wni.1

Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: N.9, G.10, F.11, G.12, R.13, I.14, G.15, N.34, D.35, P.36, F.37, I.38, E.79, R.80, S.98, T.99, G.100, V.101, F.102, S.122, A.123, S.151, C.152, H.179, T.182, A.183, N.316, E.317, Y.320 Chain D: P.191 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.14, A:Y.320 Hydrogen bonds: A:F.11, A:R.13, A:I.14, A:N.34, A:D.35, A:R.80, A:N.316 Water bridges: A:N.9, A:N.9, A:F.11, A:G.12, A:G.15, A:R.16, A:G.100, A:G.100 pi-Stacking: A:F.37 NAD.4: 30 residues within 4Å: Chain B: N.9, G.10, F.11, G.12, R.13, I.14, G.15, N.34, D.35, P.36, F.37, I.38, E.79, R.80, S.98, T.99, G.100, V.101, F.102, S.122, A.123, S.151, C.152, H.179, T.182, A.183, N.316, E.317, Y.320 Chain C: P.191 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.14, B:Y.320 Hydrogen bonds: B:N.9, B:F.11, B:R.13, B:I.14, B:N.34, B:D.35, B:R.80, B:N.316 Water bridges: B:F.11, B:G.12, B:G.15, B:T.99, B:G.100 pi-Stacking: B:F.37 NAD.5: 30 residues within 4Å: Chain B: P.191 Chain C: N.9, G.10, F.11, G.12, R.13, I.14, G.15, N.34, D.35, P.36, F.37, I.38, E.79, R.80, S.98, T.99, G.100, V.101, F.102, S.122, A.123, P.124, S.151, C.152, T.182, A.183, N.316, E.317, Y.320 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.14, C:Y.320 Hydrogen bonds: C:F.11, C:R.13, C:I.14, C:N.34, C:D.35, C:R.80, C:N.316 Water bridges: C:N.9, C:N.9, C:G.12, C:G.15, C:R.16, C:R.16, C:G.100, C:G.100, C:E.317, C:E.317 pi-Stacking: C:F.37

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: H.330 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.330, H2O.1, H2O.1 ZN.3: 2 residues within 4Å: Chain A: K.61, E.63 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.63, A:E.63 ZN.6: 4 residues within 4Å: Chain C: T.104, M.105, E.106, D.127 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.106, C:E.106, C:D.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, M.R. et al., A Dimer Interface Mutation in Glyceraldehyde-3-Phosphate Dehydrogenase Regulates Its Binding to AU-rich RNA. J.Biol.Chem. (2015)

Release Date

2014-12-03

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
A

C
B

D
C

Glyceraldehyde-3-phosphate dehydrogenase