SMTL ID : 4blr.1

P4 PROTEIN FROM BACTERIOPHAGE PHI12 IN COMPLEX WITH UTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.1: 14 residues within 4Å: Chain A: G.135, K.136, T.137, P.138, E.160, K.192, N.234, Y.288, S.292 Chain F: R.272, G.276, L.277, Q.278, N.318 18 PLIP interactions: 10 interactions with chain F, 8 interactions with chain A Hydrophobic interactions: F:Q.278 Hydrogen bonds: F:G.276, F:Q.278, F:N.318, A:K.136, A:T.137, A:T.137, A:N.234, A:Y.288 Water bridges: F:R.272, F:R.272, F:R.272, F:N.318, A:G.135 Salt bridges: F:R.272, F:R.272, A:K.192 pi-Stacking: A:Y.288 UTP.3: 14 residues within 4Å: Chain A: R.272, G.276, L.277, Q.278, N.318 Chain B: G.135, K.136, T.137, P.138, E.160, K.192, N.234, Y.288, S.292 18 PLIP interactions: 9 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:K.136, B:T.137, B:T.137, B:T.137, B:N.234, A:G.276, A:Q.278, A:N.318 Water bridges: B:G.135, B:Y.288, A:R.272, A:R.272, A:R.272 Salt bridges: B:K.192, A:R.272, A:R.272 pi-Stacking: B:Y.288 Hydrophobic interactions: A:Q.278 UTP.4: 14 residues within 4Å: Chain B: R.272, G.276, L.277, Q.278, N.318 Chain C: G.135, K.136, T.137, P.138, E.160, K.192, N.234, Y.288, S.292 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:Q.278 Hydrogen bonds: B:G.276, B:Q.278, B:N.318, C:K.136, C:T.137, C:T.137, C:N.234, C:Y.288 Water bridges: B:R.272, B:R.272, B:R.272, C:G.135, C:T.137, C:D.189 Salt bridges: B:R.272, B:R.272, C:K.192 pi-Stacking: C:Y.288 UTP.5: 14 residues within 4Å: Chain C: R.272, G.276, L.277, Q.278, N.318 Chain D: G.135, K.136, T.137, P.138, E.160, K.192, N.234, Y.288, S.292 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:Q.278 Hydrogen bonds: C:G.276, C:Q.278, C:N.318, D:K.136, D:T.137, D:T.137, D:N.234, D:Y.288 Water bridges: C:R.272, C:R.272, C:R.272, C:N.318, D:G.135 Salt bridges: C:R.272, C:R.272, D:K.192 pi-Stacking: D:Y.288 UTP.7: 14 residues within 4Å: Chain D: R.272, G.276, L.277, Q.278, N.318 Chain E: G.135, K.136, T.137, P.138, E.160, K.192, N.234, Y.288, S.292 18 PLIP interactions: 9 interactions with chain E, 9 interactions with chain D Hydrogen bonds: E:K.136, E:T.137, E:T.137, E:T.137, E:N.234, E:Y.288, D:G.276, D:Q.278, D:N.318 Water bridges: E:G.135, D:R.272, D:R.272, D:R.272 Salt bridges: E:K.192, D:R.272, D:R.272 pi-Stacking: E:Y.288 Hydrophobic interactions: D:Q.278 UTP.8: 14 residues within 4Å: Chain E: R.272, G.276, L.277, Q.278, N.318 Chain F: G.135, K.136, T.137, P.138, E.160, K.192, N.234, Y.288, S.292 19 PLIP interactions: 10 interactions with chain F, 9 interactions with chain E Hydrogen bonds: F:K.136, F:T.137, F:T.137, F:N.234, F:Y.288, E:G.276, E:Q.278, E:N.318 Water bridges: F:G.135, F:T.137, F:D.189, E:R.272, E:R.272, E:R.272 Salt bridges: F:K.192, E:R.272, E:R.272 pi-Stacking: F:Y.288 Hydrophobic interactions: E:Q.278

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 5 residues within 4Å: Chain A: A.25, P.26, G.27, S.28, D.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.31, A:D.31 DTT.6: 5 residues within 4Å: Chain D: A.25, P.26, G.27, S.28, D.31 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Omari, K. et al., Tracking in Atomic Detail the Functional Specializations in Viral Reca Helicases that Occur During Evolution. Nucleic Acids Res. (2013)

Release Date

2013-08-21

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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