SMTL ID : 3b9g.1

Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.21, D.26, T.148, D.262 Ligands: IMH.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, A:D.26, A:T.148, A:D.262, H2O.1 CA.4: 5 residues within 4Å: Chain B: D.21, D.26, T.148, D.262 Ligands: IMH.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.21, B:D.26, B:T.148, B:D.262, H2O.13

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: E.55, K.81, E.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.81, A:K.81 Water bridges: A:K.120

2 x IMH: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL(Non-covalent)

IMH.3: 12 residues within 4Å: Chain A: N.23, D.25, D.26, D.51, T.148, M.175, N.184, E.195, N.197, W.261, D.262 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.25, A:N.184, A:N.197 Water bridges: A:L.24 pi-Stacking: A:W.261 IMH.5: 13 residues within 4Å: Chain B: N.23, D.25, D.26, D.51, W.94, T.148, M.175, N.184, E.195, N.197, W.261, D.262 Ligands: CA.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.25, B:D.51, B:N.184, B:N.184, B:E.195, B:N.197 Water bridges: B:D.25 pi-Stacking: B:W.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vandemeulebroucke, A. et al., A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax. J.Biol.Chem. (2008)

Release Date

2008-04-22

Peptides

IAG-nucleoside hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IAG-nucleoside hydrolase