SMTL ID : 3gq8.2 (1 other biounit)

Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with 2-(N-cyclohexylamino)ethane sulfonic acid (CHES)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.6: 6 residues within 4Å: Chain B: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.9 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.11: 6 residues within 4Å: Chain C: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.14 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.16: 6 residues within 4Å: Chain D: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.19 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.21: 6 residues within 4Å: Chain E: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.24 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.26: 6 residues within 4Å: Chain F: D.197, D.198, N.223, N.225, E.228 Ligands: CO3.29 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: 6 residues within 4Å: Chain A: D.198, H.203, E.228, D.230, K.253 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.3 MG.7: 6 residues within 4Å: Chain B: D.198, H.203, E.228, D.230, K.253 Ligands: CO3.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.228, B:D.230, H2O.15, H2O.15 MG.12: 6 residues within 4Å: Chain C: D.198, H.203, E.228, D.230, K.253 Ligands: CO3.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.228, C:D.230, H2O.26, H2O.27 MG.17: 6 residues within 4Å: Chain D: D.198, H.203, E.228, D.230, K.253 Ligands: CO3.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.228, D:D.230, H2O.38, H2O.38 MG.22: 6 residues within 4Å: Chain E: D.198, H.203, E.228, D.230, K.253 Ligands: CO3.24 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.228, E:D.230, H2O.49, H2O.50 MG.27: 6 residues within 4Å: Chain F: D.198, H.203, E.228, D.230, K.253 Ligands: CO3.29 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.228, F:D.230, H2O.61, H2O.62

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

NHE.3: 7 residues within 4Å: Chain A: Y.171, N.223, H.255, R.281, I.283, Q.316 Ligands: CO3.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.316 Water bridges: A:N.223, A:R.281, A:R.281 Salt bridges: A:R.281 NHE.8: 7 residues within 4Å: Chain B: Y.171, N.223, H.255, R.281, I.283, Q.316 Ligands: CO3.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.316 Water bridges: B:N.223, B:R.281, B:R.281 Salt bridges: B:R.281 NHE.13: 7 residues within 4Å: Chain C: Y.171, N.223, H.255, R.281, I.283, Q.316 Ligands: CO3.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.316 Water bridges: C:N.223, C:R.281, C:R.281 Salt bridges: C:R.281 NHE.18: 7 residues within 4Å: Chain D: Y.171, N.223, H.255, R.281, I.283, Q.316 Ligands: CO3.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.316 Water bridges: D:N.223, D:R.281, D:R.281 Salt bridges: D:R.281 NHE.23: 7 residues within 4Å: Chain E: Y.171, N.223, H.255, R.281, I.283, Q.316 Ligands: CO3.24 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.316 Water bridges: E:N.223, E:R.281, E:R.281 Salt bridges: E:R.281 NHE.28: 7 residues within 4Å: Chain F: Y.171, N.223, H.255, R.281, I.283, Q.316 Ligands: CO3.29 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.316 Water bridges: F:N.223, F:R.281, F:R.281 Salt bridges: F:R.281

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

CO3.4: 10 residues within 4Å: Chain A: D.197, D.198, N.223, E.228, D.230, K.253, H.255 Ligands: CA.1, MG.2, NHE.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.223 CO3.5: 2 residues within 4Å: Chain A: R.516, Y.531 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.531 CO3.9: 10 residues within 4Å: Chain B: D.197, D.198, N.223, E.228, D.230, K.253, H.255 Ligands: CA.6, MG.7, NHE.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.223 CO3.10: 2 residues within 4Å: Chain B: R.516, Y.531 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.531 CO3.14: 10 residues within 4Å: Chain C: D.197, D.198, N.223, E.228, D.230, K.253, H.255 Ligands: CA.11, MG.12, NHE.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.223 CO3.15: 2 residues within 4Å: Chain C: R.516, Y.531 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.531 CO3.19: 10 residues within 4Å: Chain D: D.197, D.198, N.223, E.228, D.230, K.253, H.255 Ligands: CA.16, MG.17, NHE.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.223 Water bridges: D:D.198 CO3.20: 2 residues within 4Å: Chain D: R.516, Y.531 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.531, D:Y.531 CO3.24: 10 residues within 4Å: Chain E: D.197, D.198, N.223, E.228, D.230, K.253, H.255 Ligands: CA.21, MG.22, NHE.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.223 Water bridges: E:D.198 CO3.25: 2 residues within 4Å: Chain E: R.516, Y.531 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.531, E:Y.531 CO3.29: 10 residues within 4Å: Chain F: D.197, D.198, N.223, E.228, D.230, K.253, H.255 Ligands: CA.26, MG.27, NHE.28 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.223 Water bridges: F:D.198 CO3.30: 2 residues within 4Å: Chain F: R.516, Y.531 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.531, F:Y.531

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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