SMTL ID : 3o72.2 (1 other biounit)

Crystal structure of EfeB in complex with heme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: N.194, L.196, F.198, K.199, D.200, G.201, T.202, A.203, I.240, F.242, F.259, H.294, I.295, A.298, N.299, R.301, R.312, L.331, F.333, F.344, V.347, Q.348, L.351 Ligands: OXY.2 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:L.196, A:F.198, A:A.203, A:I.240, A:F.242, A:F.242, A:F.259, A:F.259, A:I.295, A:A.298, A:N.299, A:L.331, A:F.333, A:F.344, A:V.347, A:Q.348, A:L.351 Hydrogen bonds: A:G.201, A:T.202, A:A.203, A:N.299 Water bridges: A:R.261, A:R.261 Salt bridges: A:R.261, A:R.301, A:R.312 pi-Stacking: A:F.333 pi-Cation interactions: A:R.312 Metal complexes: A:H.294 HEM.3: 27 residues within 4Å: Chain B: N.194, L.196, F.198, K.199, D.200, G.201, T.202, A.203, I.240, F.242, F.259, R.261, H.294, I.295, A.298, N.299, R.301, R.312, L.331, F.333, F.344, V.347, Q.348, L.351, L.356, V.360 Ligands: OXY.4 31 PLIP interactions: 31 interactions with chain B, Hydrophobic interactions: B:L.196, B:F.198, B:A.203, B:I.240, B:F.242, B:F.259, B:F.259, B:I.295, B:A.298, B:N.299, B:L.331, B:F.333, B:F.344, B:V.347, B:Q.348, B:L.351, B:L.356, B:V.360 Hydrogen bonds: B:G.201, B:T.202, B:A.203, B:N.299 Water bridges: B:A.203, B:R.261, B:R.261 Salt bridges: B:R.261, B:R.301, B:R.312 pi-Stacking: B:F.333 pi-Cation interactions: B:R.312 Metal complexes: B:H.294

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: D.200, R.312, L.331 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.200, A:R.312 OXY.4: 5 residues within 4Å: Chain B: D.200, R.312, L.331, F.333 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes. J.Biol.Chem. (2011)

Release Date

2011-03-16

Peptides

Redox component of a tripartite ferrous iron transporter: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Redox component of a tripartite ferrous iron transporter

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