SMTL ID : 3gqa.1 (1 other biounit)

Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with cobalt ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

12 x CO: COBALT (II) ION(Non-covalent)

CO.1: 3 residues within 4Å: Chain A: H.203, E.228, D.230 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.203, A:D.230, H2O.8, H2O.8, H2O.8 CO.2: 5 residues within 4Å: Chain A: D.197, D.198, N.223, N.225, E.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.197, A:D.198, A:N.223, A:E.228, H2O.8 CO.4: 3 residues within 4Å: Chain B: H.203, E.228, D.230 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.203, B:D.230, H2O.17, H2O.17, H2O.17 CO.5: 5 residues within 4Å: Chain B: D.197, D.198, N.223, N.225, E.228 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.197, B:D.198, B:N.223, B:E.228, H2O.17 CO.7: 3 residues within 4Å: Chain C: H.203, E.228, D.230 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.203, C:D.230, H2O.25, H2O.25, H2O.25 CO.8: 5 residues within 4Å: Chain C: D.197, D.198, N.223, N.225, E.228 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.197, C:D.198, C:N.223, C:E.228, H2O.25 CO.10: 3 residues within 4Å: Chain D: H.203, E.228, D.230 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.203, D:D.230, H2O.34, H2O.34, H2O.34 CO.11: 5 residues within 4Å: Chain D: D.197, D.198, N.223, N.225, E.228 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.197, D:D.198, D:N.223, D:E.228, H2O.34 CO.13: 3 residues within 4Å: Chain E: H.203, E.228, D.230 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.203, E:D.230, H2O.42, H2O.42, H2O.42 CO.14: 5 residues within 4Å: Chain E: D.197, D.198, N.223, N.225, E.228 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.197, E:D.198, E:N.223, E:E.228, H2O.42 CO.16: 3 residues within 4Å: Chain F: H.203, E.228, D.230 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.203, F:D.230, H2O.50, H2O.51, H2O.51 CO.17: 5 residues within 4Å: Chain F: D.197, D.198, N.223, N.225, E.228 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.197, F:D.198, F:N.223, F:E.228, H2O.50

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: E.375, N.376, Y.379, Y.403, S.406 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.375, A:N.376, A:N.376, A:N.376, A:S.406 PO4.6: 5 residues within 4Å: Chain B: E.375, N.376, Y.379, Y.403, S.406 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.375, B:N.376, B:N.376, B:N.376, B:S.406 PO4.9: 5 residues within 4Å: Chain C: E.375, N.376, Y.379, Y.403, S.406 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.375, C:N.376, C:N.376, C:N.376, C:S.406 PO4.12: 5 residues within 4Å: Chain D: E.375, N.376, Y.379, Y.403, S.406 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.376, D:N.376, D:N.376, D:S.406 PO4.15: 5 residues within 4Å: Chain E: E.375, N.376, Y.379, Y.403, S.406 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.376, E:N.376, E:N.376, E:S.406 PO4.18: 5 residues within 4Å: Chain F: E.375, N.376, Y.379, Y.403, S.406 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.376, F:N.376, F:N.376, F:S.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, Y. et al., Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol.Cell (2009)

Release Date

2009-05-26

Peptides

Preneck appendage protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Preneck appendage protein

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