SMTL ID : 3kv3.1

Crystal structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH 1)from methicillin resistant Staphylococcus aureus MRSA252 complexed with NAD and G3P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, P.78, C.96, T.97, G.98, F.99, S.120, A.121, S.151, T.181, N.316, E.317, Y.320 Chain C: P.190 Ligands: 3PG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.320 Hydrogen bonds: A:F.10, A:F.10, A:R.12, A:I.13, A:N.33, A:P.78, A:N.316 Water bridges: A:N.8, A:N.8, A:G.11, A:G.14 NAD.3: 22 residues within 4Å: Chain B: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, E.77, P.78, C.96, T.97, G.98, F.99, S.120, A.121, S.151, N.316, Y.320 Chain D: P.190 Ligands: 3PG.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.320 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:N.33, B:P.78, B:N.316 Water bridges: B:G.11, B:G.14, B:Y.100, B:Y.100, B:S.151 NAD.5: 21 residues within 4Å: Chain A: P.190 Chain C: G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, P.78, C.96, T.97, G.98, F.99, S.120, A.121, S.151, T.181, N.316, Y.320 Ligands: 3PG.6 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.13, C:Y.320 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.33, C:P.78, C:N.316 Water bridges: C:G.11, C:G.14 NAD.7: 22 residues within 4Å: Chain B: P.190 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, N.33, D.34, L.35, P.78, C.96, T.97, G.98, F.99, S.120, A.121, S.151, T.181, N.316, Y.320 Ligands: 3PG.8 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.13, D:I.13, D:Y.320 Hydrogen bonds: D:F.10, D:R.12, D:I.13, D:N.33, D:P.78, D:N.316 Water bridges: D:N.8, D:N.8

4 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.2: 9 residues within 4Å: Chain A: S.150, S.151, T.152, H.178, T.181, D.183, T.211, R.234 Ligands: NAD.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.151, A:T.152, A:T.181, A:T.181, A:T.211 Water bridges: A:T.152, A:T.152, A:R.234 Salt bridges: A:H.178, A:R.234, A:R.234 3PG.4: 9 residues within 4Å: Chain B: S.150, S.151, T.152, H.178, T.181, D.183, T.211, R.234 Ligands: NAD.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.151, B:T.152, B:T.152, B:T.211, B:T.211 Water bridges: B:S.151, B:D.183, B:R.234, B:R.234, B:R.234 Salt bridges: B:H.178, B:R.234 3PG.6: 8 residues within 4Å: Chain C: S.150, S.151, T.152, H.178, T.181, D.183, R.234 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.151, C:S.151, C:S.151, C:T.152, C:T.152 Water bridges: C:D.183, C:T.211 Salt bridges: C:R.234 3PG.8: 8 residues within 4Å: Chain D: S.151, T.152, H.178, T.181, D.183, T.211, R.234 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.151, D:T.152, D:T.152, D:T.181, D:T.211 Salt bridges: D:H.178, D:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, S. et al., Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism. J.Mol.Biol. (2010)

Release Date

2010-08-18

Peptides

GAPDH: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
Q

C
R

D
P

GAPDH

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