SMTL ID : 4k1f.1

Crystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-10-mer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: T.49, Q.123, V.125, M.147 Chain F: Y.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.123 PGE.11: 5 residues within 4Å: Chain A: Y.82 Chain F: T.49, Q.123, V.125, M.147 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:Q.123, A:Y.82

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

CL.2: 2 residues within 4Å: Chain A: K.168, H.169 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: H.169, K.179 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain D: K.168, H.169 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain F: K.168, H.169 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain H: H.169, K.179 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain I: K.168, H.169 Ligand excluded by PLIP CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain B: F.50, Q.123, V.125, M.147 Chain C: Y.82 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.82 PEG.5: 3 residues within 4Å: Chain B: Y.82 Chain C: V.125, M.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.82 PEG.7: 2 residues within 4Å: Chain D: Y.82 Chain E: M.147 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.82 PEG.9: 2 residues within 4Å: Chain D: L.46 Chain E: Y.82 No protein-ligand interaction detected (PLIP) PEG.13: 5 residues within 4Å: Chain G: F.50, Q.123, V.125, M.147 Chain H: Y.82 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.82, H:Y.82 PEG.15: 3 residues within 4Å: Chain G: Y.82 Chain H: V.125, M.147 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.82, G:Y.82 PEG.17: 2 residues within 4Å: Chain I: Y.82 Chain J: M.147 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Y.82, I:Y.82 PEG.19: 2 residues within 4Å: Chain I: L.46 Chain J: Y.82 No protein-ligand interaction detected (PLIP)

2 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.4: 7 residues within 4Å: Chain B: F.165, H.169, G.180, D.181, P.182, G.194, Y.195 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.183, B:Y.195 PE8.14: 7 residues within 4Å: Chain G: F.165, H.169, G.180, D.181, P.182, G.194, Y.195 1 PLIP interactions: 1 interactions with chain G Water bridges: G:G.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brindisi, M. et al., Structure-based discovery of the first non-covalent inhibitors of Leishmania major tryparedoxin peroxidase by high throughput docking. Sci Rep (2015)

Release Date

2014-04-09

Peptides

Tryparedoxin peroxidase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Tryparedoxin peroxidase