SMTL ID : 3hx9.1

Structure of heme-degrader, MhuD (Rv3592), from Mycobacterium tuberculosis with two hemes bound in its active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 11 residues within 4Å: Chain A: R.22, R.26, A.29, V.30, W.66, A.67, A.71, H.75, A.80, N.81 Ligands: HEM.3 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:A.29, A:V.30, A:W.66, A:W.66, A:W.66, A:A.67, A:A.71, A:N.81 Salt bridges: A:R.22, A:R.26, A:R.26, A:H.78 Metal complexes: A:H.75 HEM.3: 18 residues within 4Å: Chain A: N.7, R.22, F.23, V.30, F.39, V.53, T.55, F.63, W.66, N.81, P.82, V.83, A.84, T.85, G.86, L.89 Ligands: HEM.1, CL.2 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:N.7, A:F.23, A:F.23, A:V.30, A:F.39, A:F.39, A:V.53, A:F.63, A:F.63, A:L.89 Hydrogen bonds: A:V.83, A:A.84, A:G.86, A:G.86 Salt bridges: A:R.22 HEM.4: 12 residues within 4Å: Chain B: R.22, R.26, A.29, V.30, W.66, A.67, A.71, A.74, H.75, A.80, P.82 Ligands: HEM.6 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:A.29, B:V.30, B:W.66, B:W.66, B:W.66, B:A.67, B:A.71, B:P.82 Salt bridges: B:R.22, B:R.26, B:R.26 Metal complexes: B:H.75 HEM.6: 18 residues within 4Å: Chain B: N.7, L.19, R.22, F.23, V.30, F.39, V.53, T.55, F.63, W.66, P.82, V.83, A.84, T.85, G.86, L.89 Ligands: HEM.4, CL.5 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:N.7, B:L.19, B:F.23, B:F.23, B:V.30, B:F.39, B:F.39, B:V.53, B:F.63, B:L.89 Hydrogen bonds: B:V.83, B:A.84, B:G.86, B:G.86 Salt bridges: B:R.22

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

CL.2: 5 residues within 4Å: Chain A: N.7, I.9, F.23, V.53 Ligands: HEM.3 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: N.7, I.9, F.23, V.53 Ligands: HEM.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chim, N. et al., Unusual Diheme Conformation of the Heme-Degrading Protein from Mycobacterium tuberculosis. J.Mol.Biol. (2009)

Release Date

2009-12-01

Peptides

Protein Rv3592: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein Rv3592