SMTL ID : 1nmp.1 (3 other biounits)

Structural genomics, ybgI protein, unknown function

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

11 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: H.63, H.64, H.97, H.215, E.219 Ligands: MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.64, A:H.215, A:E.219, A:E.219, H2O.3 MG.2: 5 residues within 4Å: Chain A: H.63, H.97, D.101, E.219 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.63, A:D.101, A:D.101, A:E.219 MG.3: 4 residues within 4Å: Chain B: H.63, H.97, D.101, E.219 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.6 MG.4: 5 residues within 4Å: Chain C: H.63, H.64, H.215, E.219 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.64, C:H.215, C:E.219 MG.5: 4 residues within 4Å: Chain C: H.63, D.101, E.219 Ligands: MG.4 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.9 MG.6: 6 residues within 4Å: Chain D: H.63, H.64, H.97, H.215, E.219 Ligands: MG.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.64, D:H.215, D:E.219 MG.7: 6 residues within 4Å: Chain D: H.63, H.97, D.101, N.108, E.219 Ligands: MG.6 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.12 MG.8: 6 residues within 4Å: Chain E: H.63, H.64, H.97, H.215, E.219 Ligands: MG.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.64, E:H.215, E:E.219 MG.9: 5 residues within 4Å: Chain E: H.63, D.101, N.108, E.219 Ligands: MG.8 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.16 MG.10: 6 residues within 4Å: Chain F: H.63, H.64, H.97, H.215, E.219 Ligands: MG.11 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.64, F:H.215, F:E.219, H2O.22 MG.11: 4 residues within 4Å: Chain F: H.63, D.101, E.219 Ligands: MG.10 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.20

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
A

B
B

C
C

D
D

E
E

F
F

Hypothetical protein ybgI

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