SMTL ID : 9fj2.2 (1 other biounit)

Rubrerythrin from Clostridium difficile P28

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

12 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: E.81, E.84, E.115 Chain B: E.52 Ligands: FE.4, O.7 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: A:E.81, A:E.84, A:E.115, B:E.52, O.7 FE.2: 7 residues within 4Å: Chain A: E.19, E.52, H.55 Chain B: E.84, V.111, E.115 Ligands: FE.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.19, A:E.52, A:H.55, B:E.115, B:E.115 FE.3: 4 residues within 4Å: Chain A: C.145, C.148, C.161, C.164 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.145, A:C.148, A:C.161, A:C.164 FE.4: 7 residues within 4Å: Chain A: E.84, E.115 Chain B: E.19, E.52, H.55 Ligands: FE.1, O.7 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.19, B:E.19, B:E.52, B:H.55, A:E.115 FE.5: 5 residues within 4Å: Chain A: E.52 Chain B: E.81, E.84, E.115 Ligands: FE.2 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.52, A:E.52, B:E.81, B:E.115, H2O.3 FE.6: 4 residues within 4Å: Chain B: C.145, C.148, C.161, C.164 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.145, B:C.148, B:C.161, B:C.164 FE.8: 6 residues within 4Å: Chain C: E.19, E.52, H.55 Chain D: E.115 Ligands: O.11, FE.12 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: D:E.115, C:E.19, C:E.52, C:H.55, O.11 FE.9: 4 residues within 4Å: Chain C: C.145, C.148, C.161, C.164 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.145, C:C.148, C:C.161, C:C.164 FE.10: 6 residues within 4Å: Chain C: E.81, E.84, E.115 Chain D: E.19, E.52 Ligands: FE.13 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:E.81, C:E.84, C:E.84, C:E.115, D:E.52 FE.12: 6 residues within 4Å: Chain C: E.52 Chain D: E.81, E.84, E.115 Ligands: FE.8, O.11 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:E.81, D:E.84, C:E.52, H2O.7, O.11 FE.13: 6 residues within 4Å: Chain C: V.111, E.115 Chain D: E.19, E.52, H.55 Ligands: FE.10 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Metal complexes: D:E.19, D:E.19, D:E.52, D:H.55, C:E.115 FE.14: 4 residues within 4Å: Chain D: C.145, C.148, C.161, C.164 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.145, D:C.148, D:C.161, D:C.164

2 x O: OXYGEN ATOM(Non-covalent)

O.7: 8 residues within 4Å: Chain A: E.84, E.115 Chain B: G.18, E.19, A.22, E.52 Ligands: FE.1, FE.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.18 O.11: 6 residues within 4Å: Chain C: E.19, E.52 Chain D: E.84, E.115 Ligands: FE.8, FE.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgueiro, B.A. et al., The X-ray crystal structure of the Rubrerythrin from Clostridium difficile P28 obtain by microdialysis method. To Be Published

Release Date

2025-06-11

Peptides

Rubrerythrin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Rubrerythrin

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