SMTL ID : 3lc1.1

Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.0 angstrom resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 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, C.151, T.181, N.316, E.317, Y.320 Chain D: P.190 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.13, 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:N.8, A:N.8, A:G.11, A:G.14, A:G.98, A:G.98, A:G.182, A:G.182, A:N.316 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, C.151, T.181, N.316, Y.320 Chain C: P.190 16 PLIP interactions: 16 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 Water bridges: B:N.8, B:N.8, B:G.11, B:G.14, B:G.98, B:S.120, B:G.182, B:E.317, B:E.317 NAD.4: 21 residues within 4Å: Chain B: P.190 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, C.151, T.181, N.316, Y.320 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.13, C:I.13, C:Y.320 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:N.33, C:P.78 Water bridges: C:N.8, C:N.8, C:G.11, C:G.11, C:G.14, C:G.98, C:S.120, C:G.182, C:G.182, C:G.182 NAD.5: 22 residues within 4Å: Chain A: 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, C.151, T.181, N.316, Y.320 16 PLIP interactions: 16 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 Water bridges: D:N.8, D:G.11, D:G.14, D:G.98, D:Y.100, D:S.120, D:G.182, D:G.182, D:G.182

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: A.203, E.204, P.236 Chain C: A.203, E.204 Chain D: A.203, E.204, P.236 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:E.204, A:E.204, C:A.203, D:E.204

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
P

B
R

C
O

D
Q

Glyceraldehyde-3-phosphate dehydrogenase 1