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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

3 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

3 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

3 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

3 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

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Preneck appendage protein

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