SMTL ID : 3lc2.1

Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant Staphylococcus aureus MRSA252

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Covalent)

G3H.1: 8 residues within 4Å: Chain A: S.150, C.151, T.152, H.178, T.181, T.211, G.212 Ligands: CL.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.151, A:T.152, A:T.152, A:T.152, A:G.212, A:R.234 Salt bridges: A:H.178 G3H.4: 8 residues within 4Å: Chain B: S.150, C.151, T.152, H.178, T.181, T.211, G.212 Ligands: CL.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.150, B:C.151, B:T.152, B:T.152, B:T.152, B:T.211, B:G.212 Water bridges: B:N.316, B:N.316 Salt bridges: B:H.178 G3H.7: 8 residues within 4Å: Chain C: S.150, C.151, T.152, H.178, T.181, T.211, G.212, Y.320 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.150, C:S.150, C:C.151, C:T.152, C:T.152, C:T.152, C:T.211, C:G.212 Water bridges: C:R.234, C:N.316, C:N.316 Salt bridges: C:H.178 G3H.10: 9 residues within 4Å: Chain D: S.150, C.151, T.152, H.178, T.181, T.211, G.212, A.213, R.234 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.150, D:S.150, D:C.151, D:T.152, D:T.152, D:G.212, D:A.213, D:R.234 Water bridges: D:N.316 Salt bridges: D:H.178

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

CL.2: 4 residues within 4Å: Chain A: T.181, R.198, R.234 Ligands: G3H.1 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: T.181, R.198, R.234 Ligands: G3H.4 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain C: T.181, R.198 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: G.11, R.12, I.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.12, A:I.13 Water bridges: A:G.14 GOL.6: 2 residues within 4Å: Chain B: G.11, R.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.12 Water bridges: B:G.11, B:G.11, B:I.13, B:T.97, B:G.182 GOL.9: 3 residues within 4Å: Chain C: G.11, R.12, I.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.12, C:I.13 Water bridges: C:G.11, C:G.14

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
O

B
Q

C
R

D
P

Glyceraldehyde-3-phosphate dehydrogenase 1

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