SMTL ID : 2y4e.1

X-ray crystallographic structure of E. coli ppix-EfeB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PP9: PROTOPORPHYRIN IX(Non-covalent)

PP9.1: 27 residues within 4Å: Chain A: N.209, L.211, F.213, K.214, D.215, G.216, T.217, A.218, I.255, F.257, F.274, R.276, H.309, I.310, A.313, N.314, R.316, M.325, R.327, L.346, F.348, F.359, V.362, Q.363, L.366, L.371, V.375 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:L.211, A:F.213, A:F.257, A:F.274, A:F.274, A:A.313, A:N.314, A:L.346, A:F.348, A:F.348, A:Q.363, A:L.366, A:L.371, A:V.375, A:V.375 Hydrogen bonds: A:K.214, A:G.216, A:T.217, A:A.218, A:H.309, A:N.314, A:R.316 Salt bridges: A:R.276, A:R.276, A:R.327 pi-Stacking: A:F.348 pi-Cation interactions: A:H.309, A:R.327 PP9.5: 24 residues within 4Å: Chain B: N.209, L.211, K.214, D.215, G.216, T.217, A.218, I.255, F.257, F.274, R.276, H.309, I.310, A.313, N.314, M.325, R.327, F.348, F.359, V.362, Q.363, L.366, L.371, V.375 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:L.211, B:A.218, B:I.255, B:F.257, B:F.274, B:F.274, B:A.313, B:F.348, B:F.348, B:F.359, B:F.359, B:Q.363, B:L.366, B:L.371, B:V.375, B:V.375 Hydrogen bonds: B:G.216, B:T.217, B:A.218, B:H.309, B:I.310, B:N.314 Water bridges: B:D.215, B:R.327 Salt bridges: B:R.276, B:R.316, B:R.327 pi-Stacking: B:H.309, B:H.309 pi-Cation interactions: B:R.327

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.30, N.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.31 Salt bridges: A:R.30 SO4.6: 4 residues within 4Å: Chain A: G.335, V.336 Chain B: L.152, R.190 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.336, A:V.336 Water bridges: A:G.335, A:G.335, B:R.190 Salt bridges: B:R.190

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 6 residues within 4Å: Chain A: A.150, A.151, R.187 Chain B: N.338, S.339, G.340 No protein-ligand interaction detected (PLIP) PG4.4: 8 residues within 4Å: Chain A: D.58, V.59, H.120, S.121, D.124, R.126, K.139, D.156 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.59, A:V.59, A:H.120, A:R.126, A:R.126 Water bridges: A:R.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bamford, V.A. et al., Efeb, the Peroxidase Component of the Efeuob Bacterial Fe(II) Transport System, Also Shows Novel Removal of Iron from Heme. To be Published

Release Date

2011-01-26

Peptides

PEROXIDASE YCDB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PEROXIDASE YCDB

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