SMTL ID : 3gq8.1 (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 Compare

Method

X-RAY DIFFRACTION 2.00 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.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

3 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

3 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

6 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

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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