SMTL ID : 2b4r.1

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom Resolution reveals intriguing extra electron density in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: N.17, G.18, F.19, G.20, R.21, I.22, N.42, D.43, P.44, F.45, M.46, E.87, K.88, S.106, T.107, G.108, F.110, S.130, A.131, C.161, A.192, N.327, Y.331 Ligands: AES.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.22, A:Y.331 Hydrogen bonds: A:F.19, A:R.21, A:I.22, A:N.42, A:K.88, A:N.327 Water bridges: A:N.17, A:N.17, A:G.20, A:G.23, A:G.108, A:S.130, A:A.192, A:E.328 pi-Stacking: A:F.45 NAD.4: 25 residues within 4Å: Chain B: N.17, G.18, F.19, G.20, R.21, I.22, N.42, D.43, P.44, F.45, M.46, E.87, K.88, S.106, T.107, G.108, F.110, S.130, A.131, C.161, T.191, A.192, N.327, Y.331 Ligands: AES.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.22, B:Y.331 Hydrogen bonds: B:N.17, B:F.19, B:F.19, B:R.21, B:I.22, B:N.42, B:K.88, B:K.88, B:N.327 Water bridges: B:G.20, B:G.23, B:G.108, B:S.130, B:A.192, B:E.328, B:E.328 pi-Stacking: B:F.45 NAD.7: 24 residues within 4Å: Chain C: N.17, G.18, F.19, G.20, R.21, I.22, D.43, P.44, F.45, M.46, S.106, T.107, G.108, V.109, F.110, S.130, A.131, C.161, H.188, T.191, A.192, N.327, E.328, Y.331 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.22, C:Y.331 Hydrogen bonds: C:F.19, C:F.19, C:R.21, C:I.22, C:N.327 Water bridges: C:N.17, C:N.17, C:G.20, C:G.23, C:E.328, C:E.328 pi-Stacking: C:F.45 NAD.8: 25 residues within 4Å: Chain D: N.17, G.18, F.19, G.20, R.21, I.22, N.42, D.43, P.44, F.45, E.87, K.88, S.106, T.107, G.108, F.110, S.130, A.131, C.161, H.188, T.191, A.192, N.327, Y.331 Ligands: AES.9 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.22, D:Y.331 Hydrogen bonds: D:N.17, D:F.19, D:R.21, D:I.22, D:N.42, D:K.88, D:N.327 Water bridges: D:G.20, D:G.23, D:G.108, D:S.130, D:E.328, D:E.328, A:D.198 pi-Stacking: D:F.45

3 x AES: 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE(Non-covalent)

AES.2: 4 residues within 4Å: Chain A: T.191, N.193, R.245 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) AES.5: 4 residues within 4Å: Chain B: T.191, N.193, R.245 Ligands: NAD.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.193 AES.9: 4 residues within 4Å: Chain D: T.191, A.192, N.193 Ligands: NAD.8 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: H.299, D.300, N.301, R.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.299, A:N.301, A:N.301, A:N.301 GOL.6: 4 residues within 4Å: Chain A: E.291 Chain B: G.204, D.206, W.207 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.204, B:D.206, B:W.207 Water bridges: B:R.208, A:E.291 GOL.10: 5 residues within 4Å: Chain C: G.204, K.205, D.206, W.207 Chain D: E.291 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.206, C:W.207, C:W.207 GOL.11: 5 residues within 4Å: Chain C: E.291 Chain D: G.204, K.205, D.206, W.207 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.206, D:W.207 Water bridges: D:D.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robien, M.A. et al., Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site. Proteins (2006)

Release Date

2005-10-04

Peptides

glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

glyceraldehyde-3-phosphate dehydrogenase

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