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

Crystal structure of the pre-mature bacteriophage phi29 gene product 12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.3 CA.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.5 CA.9: 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.8

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: D.198, H.203, E.228, D.230 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.203, A:E.228, A:D.230, H2O.3, H2O.3 MG.6: 1 residues within 4Å: Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: D.198, H.203, E.228, D.230 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.203, B:E.228, B:D.230, H2O.5, H2O.5 MG.10: 1 residues within 4Å: Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: D.198, H.203, E.228, D.230 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.203, C:E.228, C:D.230, H2O.8, H2O.8

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 13 residues within 4Å: Chain A: W.664, Q.665, D.697, F.698, D.699, K.702, N.703, Y.704, I.705, R.707, R.710, W.713 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.665, A:D.697, A:D.699, A:N.703, A:I.705, A:I.705, A:W.713 Salt bridges: A:R.707, A:R.710, A:R.710 pi-Stacking: A:W.664, A:W.664, A:W.664 pi-Cation interactions: A:K.702 ATP.7: 13 residues within 4Å: Chain B: W.664, Q.665, D.697, F.698, D.699, K.702, N.703, Y.704, I.705, R.707, R.710, W.713 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.665, B:D.697, B:D.699, B:N.703, B:I.705, B:I.705, B:W.713 Salt bridges: B:R.707, B:R.710, B:R.710 pi-Stacking: B:W.664, B:W.664, B:W.664 pi-Cation interactions: B:K.702 ATP.11: 13 residues within 4Å: Chain C: W.664, Q.665, D.697, F.698, D.699, K.702, N.703, Y.704, I.705, R.707, R.710, W.713 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.665, C:D.697, C:D.699, C:N.703, C:I.705, C:I.705, C:W.713 Salt bridges: C:R.707, C:R.710, C:R.710 pi-Stacking: C:W.664, C:W.664, C:W.664 pi-Cation interactions: C:K.702

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

2011-08-03

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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