SMTL ID : 4nl5.2 (1 other biounit)

Mycobacterium tuberculosis heme-degrading protein MhuD in complex with heme and cyanide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: K.5, N.7, R.22, F.23, R.26, A.27, V.30, F.39, T.55, F.63, W.66, H.75, P.82, V.83, L.89 Chain B: N.68, G.69, I.72, A.73, A.76 Ligands: CYN.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:K.5, A:F.23, A:F.39, A:T.55, A:F.63, A:W.66, A:W.66, A:L.89, B:I.72, B:I.72, B:A.73 Hydrogen bonds: A:V.83 Water bridges: A:R.26 Salt bridges: A:R.22, A:R.26 pi-Stacking: A:F.23 Metal complexes: A:H.75 HEM.4: 21 residues within 4Å: Chain A: N.68, G.69, I.72, A.76 Chain B: N.7, L.19, R.22, F.23, R.26, A.27, V.30, F.39, T.55, F.63, W.66, H.75, P.82, V.83, A.84, L.89 Ligands: CYN.5 18 PLIP interactions: 2 interactions with chain A, 16 interactions with chain B, Hydrophobic interactions: A:I.72, A:I.72, B:L.19, B:F.23, B:F.39, B:F.39, B:F.39, B:F.63, B:W.66, B:W.66, B:A.84, B:L.89 Hydrogen bonds: B:V.83, B:A.84 Salt bridges: B:R.22, B:R.26 pi-Stacking: B:F.23 Metal complexes: B:H.75

2 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 5 residues within 4Å: Chain A: N.7, I.9, F.23, V.53 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.7 CYN.5: 5 residues within 4Å: Chain B: N.7, I.9, F.23, V.53 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.7

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: R.22, H.25, R.26, H.78 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.25, A:R.26, A:H.78 ACT.6: 4 residues within 4Å: Chain B: R.22, H.25, R.26, H.78 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.25, B:R.26 Hydrogen bonds: B:R.26 Salt bridges: B:H.25, B:H.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graves, A.B. et al., Crystallographic and Spectroscopic Insights into Heme Degradation by Mycobacterium tuberculosis MhuD. Inorg.Chem. (2014)

Release Date

2014-06-25

Peptides

Heme-degrading monooxygenase HmoB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heme-degrading monooxygenase HmoB

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