SMTL ID : 1ml3.1

Evidences for a flip-flop catalytic mechanism of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase, from its crystal structure in complex with reacted irreversible inhibitor 2-(2-phosphono-ethyl)-acrylic acid 4-nitro-phenyl ester

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 19 residues within 4Å: Chain B: G.9, G.11, R.12, I.13, D.38, M.39, A.90, R.92, T.111, L.113, S.134, A.135, C.166, A.198, N.335, E.336, Y.339 Chain C: V.206 Ligands: CYX.2 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.339 Hydrogen bonds: B:R.12, B:I.13, B:M.39, B:R.92, B:N.335 Water bridges: B:N.8, B:Q.91 NAD.3: 20 residues within 4Å: Chain B: V.206 Chain C: N.8, G.9, G.11, R.12, I.13, D.38, M.39, A.90, Q.91, S.110, T.111, G.112, S.134, A.135, C.166, A.198, N.335, Y.339 Ligands: CYX.4 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.13, C:Y.339 Hydrogen bonds: C:N.8, C:R.12, C:I.13, C:D.38, C:M.39, C:Q.91, C:N.335 Water bridges: C:E.336, B:D.204 NAD.5: 24 residues within 4Å: Chain A: V.206 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, V.37, D.38, M.39, A.90, Q.91, S.110, T.111, G.112, L.113, S.134, A.135, C.166, A.198, N.335, E.336, Y.339 Ligands: CYX.6 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.13, D:Y.339 Hydrogen bonds: D:N.8, D:F.10, D:R.12, D:I.13, D:Q.91, D:Q.91, D:N.335 Water bridges: D:G.11, D:G.112, D:S.134, D:E.336, D:E.336, A:D.204

3 x CYX: (3-FORMYL-BUT-3-ENYL)-PHOSPHONIC ACID(Covalent)

CYX.2: 8 residues within 4Å: Chain B: C.166, T.167, H.194, T.197, T.199, R.249, N.335 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.197, B:T.197, B:T.197, B:T.199, B:R.249, B:R.249, B:N.335 CYX.4: 9 residues within 4Å: Chain C: S.165, C.166, T.167, H.194, T.225, T.226, S.247, R.249 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:C.166, C:T.167, C:T.226, C:T.226, C:T.226, C:S.247, C:R.249 CYX.6: 7 residues within 4Å: Chain D: C.166, H.194, T.197, T.199, R.249, N.335 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.199, D:R.249, D:R.249, D:N.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Castilho, M.S. et al., Evidence for the Two Phosphate Binding Sites of an Analogue of the Thioacyl Intermediate for the Trypanosoma cruzi Glyceraldehyde-3-phosphate Dehydrogenase-Catalyzed Reaction, from Its Crystal Structure. Biochemistry (2003)

Release Date

2003-07-08

Peptides

Glyceraldehyde 3-phosphate dehydrogenase, glycosomal: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glyceraldehyde 3-phosphate dehydrogenase, glycosomal

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