SMTL ID : 8avi.1

Crystal structure of IsdG from Bacillus cereus in complex with heme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: N.6, R.21, F.22, G.26, K.27, V.28, L.37, T.55, W.66, A.75, H.76, Q.79, M.82, N.89, I.91 Chain B: R.100 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:R.21, A:F.22, A:V.28, A:L.37, A:T.55, A:W.66, A:A.75 Hydrogen bonds: A:K.27, A:V.28, A:A.75 pi-Stacking: A:F.22 Metal complexes: A:H.76 Water bridges: B:R.100 Salt bridges: B:R.100 HEM.4: 18 residues within 4Å: Chain A: R.100 Chain B: V.4, N.6, R.21, F.22, G.26, K.27, V.28, L.37, T.55, F.63, W.66, A.75, H.76, H.78, M.82, N.89, I.91 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.4, B:V.28, B:L.37, B:T.55, B:F.63, B:W.66, B:I.91 Hydrogen bonds: B:K.27, B:V.28 Salt bridges: B:R.21, A:R.100 pi-Stacking: B:F.22, B:H.76 Metal complexes: B:H.76

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.2: 1 residues within 4Å: Chain A: M.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.1, A:M.1

1 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.3: 7 residues within 4Å: Chain A: G.36, L.37, E.38, S.54, T.55, R.56 Chain B: R.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.38, A:S.54

1 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.5: 4 residues within 4Å: Chain A: R.56 Chain B: G.36, E.38, R.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.38, B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hammerstad, M. et al., Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Antioxidants (2023)

Release Date

2023-07-12

Peptides

Heme-degrading monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heme-degrading monooxygenase

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