SMTL ID : 2vzb.1

A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein from Bacteroides fragilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-12-mer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.54, A:H.58, A:D.152, H2O.2, H2O.3, H2O.4 MG.5: 3 residues within 4Å: Chain B: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.54, B:H.58, B:D.152, H2O.5, H2O.7, H2O.7 MG.8: 3 residues within 4Å: Chain C: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.54, C:H.58, C:D.152, H2O.8, H2O.10, H2O.10 MG.11: 3 residues within 4Å: Chain D: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.54, D:H.58, D:D.152, H2O.11, H2O.13, H2O.13 MG.14: 3 residues within 4Å: Chain E: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.54, E:H.58, E:D.152, H2O.15, H2O.17, H2O.17 MG.18: 3 residues within 4Å: Chain F: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.54, F:H.58, F:D.152, H2O.18, H2O.20, H2O.20 MG.21: 3 residues within 4Å: Chain G: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:E.54, G:H.58, G:D.152, H2O.21, H2O.23, H2O.23 MG.24: 3 residues within 4Å: Chain H: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:E.54, H:H.58, H:D.152, H2O.24, H2O.26, H2O.26 MG.27: 3 residues within 4Å: Chain I: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:E.54, I:H.58, I:D.152, H2O.28, H2O.30, H2O.30 MG.31: 3 residues within 4Å: Chain J: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:E.54, J:H.58, J:D.152, H2O.31, H2O.33, H2O.33 MG.34: 3 residues within 4Å: Chain K: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:E.54, K:H.58, K:D.152, H2O.34, H2O.36, H2O.36 MG.37: 3 residues within 4Å: Chain L: E.54, H.58, D.152 6 PLIP interactions: 3 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:E.54, L:H.58, L:D.152, H2O.37, H2O.40, H2O.40

3 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 5 residues within 4Å: Chain A: Q.10, G.11, K.12, L.13, D.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.10, A:D.14 Water bridges: A:V.15 BEN.15: 5 residues within 4Å: Chain E: Q.10, G.11, K.12, L.13, D.14 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.10, E:D.14 Water bridges: E:V.15 BEN.28: 5 residues within 4Å: Chain I: Q.10, G.11, K.12, L.13, D.14 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:Q.10, I:D.14 Water bridges: I:V.15

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

FE.3: 4 residues within 4Å: Chain A: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.29, A:E.62, A:H.65, A:E.146, H2O.1 FE.4: 4 residues within 4Å: Chain A: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.62, A:E.114, A:E.146, A:H.149, H2O.3 FE.6: 5 residues within 4Å: Chain B: E.29, E.62, H.65, E.146 Ligands: FE.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.29, B:E.62, B:H.65, B:E.146, H2O.5 FE.7: 5 residues within 4Å: Chain B: E.62, E.114, E.146, H.149 Ligands: FE.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.62, B:E.114, B:E.146, B:H.149, H2O.6 FE.9: 4 residues within 4Å: Chain C: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.29, C:E.62, C:H.65, C:E.146, H2O.7 FE.10: 4 residues within 4Å: Chain C: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.62, C:E.114, C:E.146, C:H.149, H2O.8 FE.12: 4 residues within 4Å: Chain D: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.29, D:E.62, D:H.65, D:E.146, H2O.11 FE.13: 4 residues within 4Å: Chain D: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.62, D:E.114, D:E.146, D:H.149, H2O.12 FE.16: 4 residues within 4Å: Chain E: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.29, E:E.62, E:H.65, E:E.146, H2O.14 FE.17: 4 residues within 4Å: Chain E: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.62, E:E.114, E:E.146, E:H.149, H2O.16 FE.19: 5 residues within 4Å: Chain F: E.29, E.62, H.65, E.146 Ligands: FE.20 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.29, F:E.62, F:H.65, F:E.146, H2O.18 FE.20: 5 residues within 4Å: Chain F: E.62, E.114, E.146, H.149 Ligands: FE.19 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.62, F:E.114, F:E.146, F:H.149, H2O.19 FE.22: 4 residues within 4Å: Chain G: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.29, G:E.62, G:H.65, G:E.146, H2O.20 FE.23: 4 residues within 4Å: Chain G: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.62, G:E.114, G:E.146, G:H.149, H2O.21 FE.25: 4 residues within 4Å: Chain H: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.29, H:E.62, H:H.65, H:E.146, H2O.24 FE.26: 4 residues within 4Å: Chain H: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.62, H:E.114, H:E.146, H:H.149, H2O.26 FE.29: 4 residues within 4Å: Chain I: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.29, I:E.62, I:H.65, I:E.146, H2O.27 FE.30: 4 residues within 4Å: Chain I: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.62, I:E.114, I:E.146, I:H.149, H2O.29 FE.32: 5 residues within 4Å: Chain J: E.29, E.62, H.65, E.146 Ligands: FE.33 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.29, J:E.62, J:H.65, J:E.146, H2O.32 FE.33: 5 residues within 4Å: Chain J: E.62, E.114, E.146, H.149 Ligands: FE.32 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.62, J:E.114, J:E.146, J:H.149, H2O.32 FE.35: 4 residues within 4Å: Chain K: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.29, K:E.62, K:H.65, K:E.146, H2O.34 FE.36: 4 residues within 4Å: Chain K: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.62, K:E.114, K:E.146, K:H.149, H2O.35 FE.38: 4 residues within 4Å: Chain L: E.29, E.62, H.65, E.146 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.29, L:E.62, L:H.65, L:E.146, H2O.38 FE.39: 4 residues within 4Å: Chain L: E.62, E.114, E.146, H.149 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.62, L:E.114, L:E.146, L:H.149, H2O.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gauss, G.H. et al., Characterization of the Bacteroides Fragilis Bfr Gene Product Identifies a Bacterial Dps-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily. J.Bacteriol. (2012)

Release Date

2009-11-17

Peptides

PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN