SMTL ID : 2vhu.1

P4 PROTEIN FROM BACTERIOPHAGE PHI12 K241C MUTANT IN COMPLEX WITH ADP AND MGCL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: N.133, S.134, G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Chain F: G.276, L.277, Q.278, R.279 Ligands: MG.2 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:N.133, A:S.134, A:G.135, A:K.136, A:T.137, A:N.234, A:Y.288, A:S.292 pi-Stacking: A:Y.288, A:Y.288 Salt bridges: F:R.272, F:R.279 ADP.3: 14 residues within 4Å: Chain A: G.276, L.277, Q.278, R.279 Chain B: N.133, S.134, G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.4 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.133, B:N.133, B:S.134, B:G.135, B:K.136, B:T.137, B:N.234, B:S.292, A:R.279 Water bridges: B:N.133 Salt bridges: B:K.136 pi-Stacking: B:Y.288, B:Y.288 ADP.5: 14 residues within 4Å: Chain B: G.276, L.277, Q.278, R.279 Chain C: N.133, S.134, G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.6 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Salt bridges: B:R.272, B:R.279 Hydrogen bonds: C:N.133, C:S.134, C:G.135, C:K.136, C:T.137, C:N.234 Water bridges: C:Y.288 pi-Stacking: C:Y.288, C:Y.288 ADP.7: 14 residues within 4Å: Chain C: G.276, L.277, Q.278, R.279 Chain D: N.133, S.134, G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.8 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.133, D:S.134, D:G.135, D:K.136, D:T.137, D:N.234, D:S.292 pi-Stacking: D:Y.288, D:Y.288 Salt bridges: C:R.272, C:R.279 ADP.9: 14 residues within 4Å: Chain D: G.276, L.277, Q.278, R.279 Chain E: N.133, S.134, G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.10 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.133, E:N.133, E:S.134, E:G.135, E:K.136, E:T.137, E:N.234, E:Y.288, E:S.292, D:R.279 Water bridges: E:N.133 Salt bridges: E:K.136 pi-Stacking: E:Y.288, E:Y.288 ADP.11: 14 residues within 4Å: Chain E: G.276, L.277, Q.278, R.279 Chain F: N.133, S.134, G.135, K.136, T.137, P.138, N.234, Y.288, S.292 Ligands: MG.12 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain F Salt bridges: E:R.272, E:R.279 Hydrogen bonds: F:N.133, F:S.134, F:G.135, F:K.136, F:T.137, F:N.234, F:Y.288 pi-Stacking: F:Y.288, F:Y.288

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.137, D.189, S.232, N.234 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.137 MG.4: 4 residues within 4Å: Chain B: T.137, D.189, S.232 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.137 MG.6: 4 residues within 4Å: Chain C: T.137, D.189, S.232 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.137 MG.8: 5 residues within 4Å: Chain D: T.137, D.189, S.232, N.234 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.137 MG.10: 4 residues within 4Å: Chain E: T.137, D.189, S.232 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.137 MG.12: 4 residues within 4Å: Chain F: T.137, D.189, S.232 Ligands: ADP.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

2007-12-11

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