SMTL ID : 2vhq.1

P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A MUTANT IN COMPLEX WITH ATP AND MG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: G.135, K.136, T.137, P.138, E.160, N.234, Y.288, S.292 Chain F: R.272, G.276, L.277, Q.278, R.279, N.318 Ligands: MG.2 22 PLIP interactions: 13 interactions with chain F, 9 interactions with chain A Hydrogen bonds: F:Q.278, F:R.279, F:R.279, F:N.318, A:K.136, A:T.137, A:T.137, A:N.234, A:Y.288, A:S.292 Water bridges: F:R.272, F:R.272, F:G.276, F:G.276, F:R.279, A:E.160 Salt bridges: F:R.272, F:R.272, F:R.279, F:R.279 pi-Stacking: A:Y.288, A:Y.288 ATP.3: 14 residues within 4Å: Chain A: R.272, G.276, L.277, Q.278, R.279, N.318 Chain B: G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.4 23 PLIP interactions: 11 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:K.136, B:T.137, B:T.137, B:N.234, B:S.292, A:R.279, A:N.318 Water bridges: B:E.160, B:Y.288, B:Y.288, A:R.272, A:R.272, A:R.272, A:G.276, A:G.276 Salt bridges: B:K.136, A:R.272, A:R.272, A:R.279, A:R.279, A:R.279 pi-Stacking: B:Y.288, B:Y.288 ATP.5: 15 residues within 4Å: Chain B: R.272, G.276, L.277, Q.278, R.279, K.317, N.318 Chain C: G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.6 22 PLIP interactions: 14 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:Q.278, B:N.318, C:K.136, C:T.137, C:T.137, C:N.234, C:S.292 Water bridges: B:R.272, B:R.272, B:R.272, B:G.276, B:G.276, B:I.316, B:K.317, C:Y.288 Salt bridges: B:R.272, B:R.272, B:R.279, B:R.279, B:R.279 pi-Stacking: C:Y.288, C:Y.288 ATP.7: 15 residues within 4Å: Chain C: R.272, G.276, L.277, Q.278, R.279, N.318 Chain D: G.135, K.136, T.137, P.138, E.160, N.234, Y.288, S.292 Ligands: MG.8 22 PLIP interactions: 9 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:K.136, D:T.137, D:T.137, D:N.234, D:S.292, C:Q.278, C:R.279, C:R.279, C:N.318 Water bridges: D:E.160, D:Y.288, C:R.272, C:R.272, C:G.276, C:G.276, C:R.279 pi-Stacking: D:Y.288, D:Y.288 Salt bridges: C:R.272, C:R.272, C:R.279, C:R.279 ATP.9: 14 residues within 4Å: Chain D: R.272, G.276, L.277, Q.278, R.279, N.318 Chain E: G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.10 23 PLIP interactions: 12 interactions with chain D, 11 interactions with chain E Hydrogen bonds: D:R.279, D:N.318, E:K.136, E:T.137, E:T.137, E:N.234, E:Y.288, E:S.292 Water bridges: D:R.272, D:R.272, D:R.272, D:G.276, D:G.276, E:G.135, E:E.160 Salt bridges: D:R.272, D:R.272, D:R.279, D:R.279, D:R.279, E:K.136 pi-Stacking: E:Y.288, E:Y.288 ATP.11: 15 residues within 4Å: Chain E: R.272, G.276, L.277, Q.278, R.279, K.317, N.318 Chain F: G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.12 22 PLIP interactions: 14 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:Q.278, E:N.318, F:K.136, F:T.137, F:T.137, F:N.234, F:Y.288, F:S.292 Water bridges: E:R.272, E:R.272, E:R.272, E:G.276, E:G.276, E:I.316, E:K.317 Salt bridges: E:R.272, E:R.272, E:R.279, E:R.279, E:R.279 pi-Stacking: F:Y.288, F:Y.288

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.137 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.137 MG.4: 2 residues within 4Å: Chain B: T.137 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.137 MG.6: 2 residues within 4Å: Chain C: T.137 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.137 MG.8: 2 residues within 4Å: Chain D: T.137 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.137 MG.10: 2 residues within 4Å: Chain E: T.137 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.137 MG.12: 2 residues within 4Å: Chain F: T.137 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kainov, D.E. et al., Structural Basis of Mechanochemical Coupling in a Hexameric Molecular Motor. J.Biol.Chem. (2008)

Release Date

2007-12-04

Peptides

NTPASE P4: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NTPASE P4

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