SMTL ID : 3k9q.1

Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 from Methicillin resistant Staphylococcus aureus (MRSA252) at 2.5 angstrom resolution

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: 24 residues within 4Å: Chain A: 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, G.151, T.181, N.316, E.317, Y.320 Chain C: P.190 Ligands: GOL.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.320 Hydrogen bonds: A:F.10, A:R.12, A:I.13, A:N.33, A:P.78 Water bridges: A:G.11, A:G.14, A:N.316 NAD.3: 23 residues within 4Å: Chain B: 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, G.151, N.316, E.317, Y.320 Chain D: P.190 Ligands: GOL.4, CL.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.320 Hydrogen bonds: B:R.12, B:I.13, B:N.33, B:P.78, B:N.316 Water bridges: B:N.8, B:N.8, B:G.11, B:G.14 NAD.6: 25 residues within 4Å: Chain A: P.190 Chain C: 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, Y.100, S.120, A.121, G.151, T.181, N.316, E.317, Y.320 Ligands: GOL.7 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.13, C:Y.320 Hydrogen bonds: C:F.10, C:F.10, C:R.12, C:I.13, C:N.33, C:P.78 Water bridges: C:N.8, C:G.11, C:G.14, C:Y.100, C:G.182, C:G.182 NAD.8: 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, E.77, P.78, C.96, T.97, G.98, F.99, S.120, A.121, G.151, T.181, N.316, Y.320 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.13, D:Y.320 Hydrogen bonds: D:F.10, D:F.10, D:R.12, D:I.13, D:N.33, D:P.78 Water bridges: D:G.14, D:G.98, D:G.98

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.150, G.151, T.152, H.178, T.211, Y.314 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.151, A:T.152, A:T.211, A:T.211, A:Y.314 GOL.4: 11 residues within 4Å: Chain B: R.12, A.179, Y.180, T.181, G.182, A.238, T.239, N.316, E.317 Chain D: Q.187 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.182, B:A.238, B:E.317, B:E.317 GOL.7: 7 residues within 4Å: Chain C: P.122, S.150, G.151, T.152, H.178, Y.314 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.151, C:T.152, C:T.152, C:Y.314, C:Y.314 Water bridges: C:T.181, C:R.234

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain B: T.181, R.234 Ligands: NAD.3 Ligand excluded by PLIP

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

Glyceraldehyde-3-phosphate dehydrogenase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
O

C
P

D
R

Glyceraldehyde-3-phosphate dehydrogenase 1

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