SMTL ID : 1nmo.2 (3 other biounits)

Structural genomics, protein ybgI, unknown function

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: H.63, H.64, H.215, E.219 Ligands: FE.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.64, A:H.215, A:E.219 FE.2: 4 residues within 4Å: Chain A: H.63, D.101, E.219 Ligands: FE.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.63, A:D.101, A:D.101, A:E.219, H2O.3 FE.3: 4 residues within 4Å: Chain B: H.64, H.215, E.219 Ligands: FE.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.64, B:H.215, B:E.219 FE.4: 5 residues within 4Å: Chain B: H.63, H.97, D.101, E.219 Ligands: FE.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.63, B:D.101, B:D.101, B:E.219, H2O.7 FE.5: 5 residues within 4Å: Chain C: H.63, H.64, H.215, E.219 Ligands: FE.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.64, C:H.215, C:E.219 FE.6: 4 residues within 4Å: Chain C: H.63, D.101, E.219 Ligands: FE.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.63, C:D.101, C:D.101, C:E.219, H2O.11 FE.7: 4 residues within 4Å: Chain D: H.64, H.215, E.219 Ligands: FE.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.64, D:H.215, D:E.219 FE.8: 5 residues within 4Å: Chain D: H.63, H.97, D.101, E.219 Ligands: FE.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.63, D:D.101, D:D.101, D:E.219, H2O.15 FE.9: 5 residues within 4Å: Chain E: H.63, H.64, H.215, E.219 Ligands: FE.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.64, E:H.215, E:E.219 FE.10: 4 residues within 4Å: Chain E: H.63, D.101, E.219 Ligands: FE.9 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.63, E:D.101, E:D.101, E:E.219, H2O.19 FE.11: 4 residues within 4Å: Chain F: H.64, H.215, E.219 Ligands: FE.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.64, F:H.215, F:E.219 FE.12: 5 residues within 4Å: Chain F: H.63, H.97, D.101, E.219 Ligands: FE.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.63, F:D.101, F:D.101, F:E.219, H2O.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ladner, J.E. et al., Crystal Structure of Escherichia coli Protein ybgI, a toroidal structure with a dinuclear metal site. BMC Struct.Biol. (2003)

Release Date

2004-01-20

Peptides

Hypothetical protein ybgI: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

Hypothetical protein ybgI

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