SMTL ID : 4fni.1

Crystal structure of IsdI-W66Y in complex with heme and cyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: N.8, L.10, R.23, F.24, N.26, R.27, Q.28, G.29, I.30, M.39, F.65, Y.68, L.69, F.74, A.77, H.78, V.81, L.83, I.94, N.97, V.99 Ligands: CYN.2 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.10, A:R.23, A:F.24, A:I.30, A:F.65, A:F.65, A:F.74, A:V.81, A:V.81, A:L.83, A:I.94, A:V.99 Hydrogen bonds: A:N.26, A:Q.28, A:Q.28, A:I.30 Water bridges: A:R.23, A:R.23 Salt bridges: A:R.23, A:R.27 pi-Stacking: A:F.24, A:F.74 Metal complexes: A:H.78 HEM.3: 21 residues within 4Å: Chain B: N.8, R.23, F.24, R.27, Q.28, G.29, I.30, M.39, I.55, T.57, F.65, Y.68, F.74, A.77, H.78, V.81, L.83, I.94, N.97, V.99 Ligands: CYN.4 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:R.23, B:F.24, B:I.30, B:I.55, B:T.57, B:F.65, B:F.74, B:V.81, B:V.81, B:L.83, B:I.94, B:V.99 Hydrogen bonds: B:Q.28, B:Q.28, B:I.30 Water bridges: B:R.23, B:R.23, B:Y.68 Salt bridges: B:R.23, B:R.27 pi-Stacking: B:F.74 Metal complexes: B:H.78

2 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 5 residues within 4Å: Chain A: N.8, F.24, I.55, H.78 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.8 Water bridges: A:N.8 CYN.4: 5 residues within 4Å: Chain B: N.8, F.24, I.55, H.78 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.8

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ukpabi, G. et al., Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling. J.Biol.Chem. (2012)

Release Date

2012-08-22

Peptides

Heme-degrading monooxygenase isdI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heme-degrading monooxygenase isdI

Related Entries With Identical Sequence