SMTL ID : 3l4s.1

Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant Staphylococcus aureus MRSA252 complexed with NAD and G3P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

3PG.1: 8 residues within 4Å: Chain A: S.150, G.151, T.152, H.178, D.183, R.234, N.316 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.151, A:T.152, A:T.152 Salt bridges: A:H.178, A:R.234 3PG.4: 10 residues within 4Å: Chain B: S.150, G.151, T.152, H.178, T.181, D.183, R.234, Y.314, N.316 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.151, B:T.152, B:T.152, B:T.152, B:R.234 Salt bridges: B:H.178 3PG.6: 10 residues within 4Å: Chain C: S.150, G.151, T.152, H.178, T.181, D.183, R.234, Y.314, N.316 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.151, C:T.152, C:T.152, C:T.152, C:R.234 Salt bridges: C:H.178, C:R.234 3PG.8: 10 residues within 4Å: Chain D: S.150, G.151, T.152, H.178, T.181, D.183, R.234, Y.314, N.316 Ligands: NAD.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.150, D:G.151, D:T.152, D:T.152, D:T.181 Water bridges: D:G.182 Salt bridges: D:H.178, D:R.234

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

NAD.2: 22 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, G.151, T.181, N.316, Y.320 Chain B: P.190 Ligands: 3PG.1 11 PLIP interactions: 11 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, A:N.316 Water bridges: A:G.11, A:G.14, A:G.182 NAD.3: 22 residues within 4Å: Chain A: P.190 Chain B: 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, G.151, T.181, N.316, E.317, Y.320 Ligands: 3PG.4 12 PLIP interactions: 12 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:N.8, B:G.11, B:G.14, B:Y.100 NAD.5: 22 residues within 4Å: Chain C: 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 Chain D: P.190 Ligands: 3PG.6 11 PLIP interactions: 11 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:E.317, C:E.317 NAD.7: 22 residues within 4Å: Chain C: P.190 Chain D: 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, Y.100, S.120, A.121, G.151, T.181, N.316, Y.320 Ligands: 3PG.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: 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:G.11, D:G.182, D:G.182, D:G.182, D:G.182

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
P

C
O

D
R

Glyceraldehyde-3-phosphate dehydrogenase 1

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