SMTL ID : 3gq9.2 (1 other biounit)

Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in an apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

12 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: D.197, D.198, N.223, N.225, E.228 Ligands: NA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.197, A:N.225 NA.2: 5 residues within 4Å: Chain A: D.198, H.203, E.228, D.230 Ligands: NA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.203, A:K.253 NA.4: 6 residues within 4Å: Chain B: D.197, D.198, N.223, N.225, E.228 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.223, B:N.225 NA.5: 5 residues within 4Å: Chain B: D.198, H.203, E.228, D.230 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.253, B:K.253 NA.7: 6 residues within 4Å: Chain C: D.197, D.198, N.223, N.225, E.228 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.198, C:N.225 NA.8: 5 residues within 4Å: Chain C: D.198, H.203, E.228, D.230 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.197, C:K.253 NA.10: 6 residues within 4Å: Chain D: D.197, D.198, N.223, N.225, E.228 Ligands: NA.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.197, D:N.225, D:E.228 NA.11: 5 residues within 4Å: Chain D: D.198, H.203, E.228, D.230 Ligands: NA.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.228, D:D.230, D:K.253, D:K.253 Water bridges: D:Y.169 NA.13: 6 residues within 4Å: Chain E: D.197, D.198, N.223, N.225, E.228 Ligands: NA.14 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.197, E:N.225, E:E.228 NA.14: 5 residues within 4Å: Chain E: D.198, H.203, E.228, D.230 Ligands: NA.13 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.228, E:D.230, E:K.253, E:K.253 Water bridges: E:Y.169 NA.16: 6 residues within 4Å: Chain F: D.197, D.198, N.223, N.225, E.228 Ligands: NA.17 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.197, F:N.225, F:E.228 NA.17: 5 residues within 4Å: Chain F: D.198, H.203, E.228, D.230 Ligands: NA.16 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:D.197, F:E.228, F:D.230, F:K.253 Water bridges: F:Y.169

6 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.3: 7 residues within 4Å: Chain A: R.276, H.286, T.320, R.322, E.349, Q.355, F.356 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.286 Hydrogen bonds: A:Q.355 Salt bridges: A:R.276, A:R.322 pi-Stacking: A:F.356 NHE.6: 7 residues within 4Å: Chain B: R.276, H.286, T.320, R.322, E.349, Q.355, F.356 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.286 Hydrogen bonds: B:Q.355 Salt bridges: B:R.276, B:R.322 pi-Stacking: B:F.356 NHE.9: 7 residues within 4Å: Chain C: R.276, H.286, T.320, R.322, E.349, Q.355, F.356 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:H.286 Hydrogen bonds: C:Q.355 Salt bridges: C:R.276, C:R.322 pi-Stacking: C:F.356 NHE.12: 7 residues within 4Å: Chain D: R.276, H.286, T.320, R.322, E.349, Q.355, F.356 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:H.286 Hydrogen bonds: D:Q.355 Water bridges: D:T.320, D:T.320 Salt bridges: D:R.276, D:R.322 pi-Stacking: D:F.356 NHE.15: 7 residues within 4Å: Chain E: R.276, H.286, T.320, R.322, E.349, Q.355, F.356 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:H.286 Hydrogen bonds: E:Q.355 Water bridges: E:T.320, E:T.320 Salt bridges: E:R.276, E:R.322 pi-Stacking: E:F.356 NHE.18: 7 residues within 4Å: Chain F: R.276, H.286, T.320, R.322, E.349, Q.355, F.356 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:H.286 Hydrogen bonds: F:Q.355 Water bridges: F:T.320, F:T.320 Salt bridges: F:R.276, F:R.322 pi-Stacking: F:F.356

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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