SMTL ID : 3gq7.2 (1 other biounit)

Crystal Structure of the Bacteriophage Phi29 Gene Product 12 N-terminal Fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.197, A:D.198, A:D.198, A:N.223, A:E.228 CA.5: 6 residues within 4Å: Chain B: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.197, B:D.198, B:D.198, B:N.223, B:E.228 CA.9: 6 residues within 4Å: Chain C: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.197, C:D.198, C:D.198, C:N.223, C:E.228 CA.13: 6 residues within 4Å: Chain D: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.16 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.197, D:D.198, D:D.198, D:N.223, D:E.228 CA.17: 6 residues within 4Å: Chain E: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.20 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.197, E:D.198, E:D.198, E:N.223, E:E.228 CA.21: 6 residues within 4Å: Chain F: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.24 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.197, F:D.198, F:D.198, F:N.223, F:E.228

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.198, H.203, E.228, D.230 Ligands: CO3.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.228, A:D.230, H2O.3, H2O.4 MG.6: 5 residues within 4Å: Chain B: D.198, H.203, E.228, D.230 Ligands: CO3.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.228, B:D.230, H2O.20, H2O.20 MG.10: 5 residues within 4Å: Chain C: D.198, H.203, E.228, D.230 Ligands: CO3.12 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.228, C:D.230, H2O.37, H2O.37 MG.14: 5 residues within 4Å: Chain D: D.198, H.203, E.228, D.230 Ligands: CO3.16 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.228, D:D.230, H2O.54, H2O.54 MG.18: 5 residues within 4Å: Chain E: D.198, H.203, E.228, D.230 Ligands: CO3.20 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.228, E:D.230, H2O.70, H2O.71 MG.22: 5 residues within 4Å: Chain F: D.198, H.203, E.228, D.230 Ligands: CO3.24 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.228, F:D.230, H2O.87, H2O.88

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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.375, A:N.376, A:N.376, A:Y.379, A:S.406 Water bridges: A:S.406 PO4.7: 5 residues within 4Å: Chain B: E.375, N.376, Y.379, Y.403, S.406 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.375, B:N.376, B:N.376, B:Y.379, B:S.406 Water bridges: B:S.406 PO4.11: 5 residues within 4Å: Chain C: E.375, N.376, Y.379, Y.403, S.406 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.375, C:N.376, C:N.376, C:Y.379, C:S.406 Water bridges: C:S.406 PO4.15: 5 residues within 4Å: Chain D: E.375, N.376, Y.379, Y.403, S.406 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.376, D:N.376, D:Y.379, D:S.406 Water bridges: D:Y.379, D:S.406 PO4.19: 5 residues within 4Å: Chain E: E.375, N.376, Y.379, Y.403, S.406 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.376, E:N.376, E:Y.379, E:S.406 Water bridges: E:Y.379, E:S.406 PO4.23: 5 residues within 4Å: Chain F: E.375, N.376, Y.379, Y.403, S.406 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.376, F:N.376, F:Y.379, F:S.406 Water bridges: F:Y.379, F:S.406

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.4: 8 residues within 4Å: Chain A: D.197, D.198, N.223, E.228, K.253, H.255 Ligands: CA.1, MG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.198, A:N.223 Water bridges: A:N.223 CO3.8: 8 residues within 4Å: Chain B: D.197, D.198, N.223, E.228, K.253, H.255 Ligands: CA.5, MG.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.198, B:N.223 Water bridges: B:N.223 CO3.12: 8 residues within 4Å: Chain C: D.197, D.198, N.223, E.228, K.253, H.255 Ligands: CA.9, MG.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.198, C:N.223 Water bridges: C:N.223 CO3.16: 8 residues within 4Å: Chain D: D.197, D.198, N.223, E.228, K.253, H.255 Ligands: CA.13, MG.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.198, D:N.223 Water bridges: D:N.223 CO3.20: 8 residues within 4Å: Chain E: D.197, D.198, N.223, E.228, K.253, H.255 Ligands: CA.17, MG.18 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.198, E:N.223 Water bridges: E:N.223 CO3.24: 8 residues within 4Å: Chain F: D.197, D.198, N.223, E.228, K.253, H.255 Ligands: CA.21, MG.22 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.198, F:N.223 Water bridges: F:N.223

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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