SMTL ID : 3mng.1

wild type human PrxV with DTT bound as a competitive inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x D1D: (4S,5S)-1,2-DITHIANE-4,5-DIOL(Non-covalent)

D1D.1: 8 residues within 4Å: Chain A: P.52, T.56, P.57, G.58, C.59, F.132, R.139, T.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.58, A:C.59, A:R.139 D1D.12: 8 residues within 4Å: Chain B: P.52, T.56, P.57, G.58, C.59, F.132, R.139, T.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.56, B:G.58, B:C.59, B:R.139

16 x BR: BROMIDE ION(Non-covalent)

BR.2: 1 residues within 4Å: Chain A: S.130 Ligand excluded by PLIP BR.3: 2 residues within 4Å: Chain A: G.66, P.167 Ligand excluded by PLIP BR.4: 2 residues within 4Å: Chain A: G.160, L.161 Ligand excluded by PLIP BR.5: 4 residues within 4Å: Chain A: R.98, K.101, A.102, E.103 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: L.124, D.125, S.127 Ligand excluded by PLIP BR.7: 2 residues within 4Å: Chain A: S.60, H.100 Ligand excluded by PLIP BR.8: 2 residues within 4Å: Chain A: K.16, V.17 Ligand excluded by PLIP BR.9: 2 residues within 4Å: Chain A: E.39, L.40 Ligand excluded by PLIP BR.13: 1 residues within 4Å: Chain B: S.130 Ligand excluded by PLIP BR.14: 2 residues within 4Å: Chain B: G.66, P.167 Ligand excluded by PLIP BR.15: 2 residues within 4Å: Chain B: G.160, L.161 Ligand excluded by PLIP BR.16: 4 residues within 4Å: Chain B: R.98, K.101, A.102, E.103 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain B: L.124, D.125, S.127 Ligand excluded by PLIP BR.18: 2 residues within 4Å: Chain B: S.60, H.100 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain B: K.16, V.17 Ligand excluded by PLIP BR.20: 2 residues within 4Å: Chain B: E.39, L.40 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: T.162, C.163, N.168 No protein-ligand interaction detected (PLIP) GOL.11: 3 residues within 4Å: Chain A: K.138, L.152, V.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.138, A:K.138 Water bridges: A:I.15, A:I.15 GOL.21: 3 residues within 4Å: Chain B: T.162, C.163, N.168 No protein-ligand interaction detected (PLIP) GOL.22: 3 residues within 4Å: Chain B: K.138, L.152, V.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.138, B:K.138 Water bridges: B:I.15, B:I.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, A. et al., Structural Evidence that Peroxiredoxin Catalytic Power Is Based on Transition-State Stabilization. J.Mol.Biol. (2010)

Release Date

2010-08-04

Peptides

Peroxiredoxin-5, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peroxiredoxin-5, mitochondrial