SMTL ID : 3i5a.1

Crystal structure of full-length WpsR from Pseudomonas syringae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

8 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.1: 13 residues within 4Å: Chain A: S.237, C.238, S.239, R.240, D.243, L.257, T.260, G.264, L.267, L.268, K.271 Chain D: R.196 Ligands: C2E.2 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:R.196, D:R.196, A:S.239, A:R.240, A:T.260, A:S.261 Salt bridges: A:R.240, A:D.243, A:K.271 pi-Cation interactions: A:R.240 C2E.2: 7 residues within 4Å: Chain A: S.239, R.240, P.241 Chain D: T.195, R.196, V.305 Ligands: C2E.1 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.196, D:R.196, A:R.240 pi-Cation interactions: D:R.196 Water bridges: A:S.239 C2E.4: 13 residues within 4Å: Chain B: S.237, C.238, S.239, R.240, D.243, L.257, T.260, G.264, L.267, L.268, K.271 Chain C: R.196 Ligands: C2E.5 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.239, B:R.240, B:T.260, B:S.261, C:R.196, C:R.196 Salt bridges: B:R.240, B:D.243, B:K.271 pi-Cation interactions: B:R.240 C2E.5: 7 residues within 4Å: Chain B: S.239, R.240, P.241 Chain C: T.195, R.196, V.305 Ligands: C2E.4 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.240, C:R.196, C:R.196 Water bridges: B:S.239 pi-Cation interactions: C:R.196 C2E.7: 13 residues within 4Å: Chain B: R.196 Chain C: S.237, C.238, S.239, R.240, D.243, L.257, T.260, G.264, L.267, L.268, K.271 Ligands: C2E.8 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:R.196, B:R.196, C:S.239, C:R.240, C:T.260, C:T.260, C:S.261 Salt bridges: C:R.240, C:D.243, C:K.271 pi-Cation interactions: C:R.240 C2E.8: 7 residues within 4Å: Chain B: T.195, R.196, V.305 Chain C: S.239, R.240, P.241 Ligands: C2E.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.196, B:R.196, C:R.240 pi-Cation interactions: B:R.196 Water bridges: C:S.239 C2E.10: 13 residues within 4Å: Chain A: R.196 Chain D: S.237, C.238, S.239, R.240, D.243, L.257, T.260, G.264, L.267, L.268, K.271 Ligands: C2E.11 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain D Hydrogen bonds: A:R.196, A:R.196, D:S.239, D:R.240, D:T.260, D:T.260, D:S.261 Salt bridges: D:R.240, D:D.243, D:K.271 pi-Cation interactions: D:R.240 C2E.11: 7 residues within 4Å: Chain A: T.195, R.196, V.305 Chain D: S.239, R.240, P.241 Ligands: C2E.10 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.196, A:R.196, D:R.240 pi-Cation interactions: A:R.196 Water bridges: D:S.239

4 x SR: STRONTIUM ION(Non-functional Binders)

SR.3: 5 residues within 4Å: Chain A: D.24, Q.25, D.68, V.70, K.120 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.24, A:D.68, A:V.70 SR.6: 5 residues within 4Å: Chain B: D.24, Q.25, D.68, V.70, K.120 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.24, B:D.68, B:V.70 SR.9: 5 residues within 4Å: Chain C: D.24, Q.25, D.68, V.70, K.120 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.24, C:D.68, C:V.70 SR.12: 5 residues within 4Å: Chain D: D.24, Q.25, D.68, V.70, K.120 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.24, D:D.68, D:V.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De, N. et al., Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR. J.Mol.Biol. (2009)

Release Date

2009-08-18

Peptides

Response regulator/GGDEF domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Response regulator/GGDEF domain protein