SMTL ID : 2v0n.1

ACTIVATED RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP AND GTP- ALPHA-S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-dimer

Ligands

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.1: 7 residues within 4Å: Chain A: D.52, V.53, M.54, T.82, A.83, K.104 Ligands: MG.2 No protein-ligand interaction detected (PLIP) BEF.11: 7 residues within 4Å: Chain B: D.52, V.53, M.54, T.82, A.83, K.104 Ligands: MG.12 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.9, D.52, M.54 Ligands: BEF.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:D.9, A:D.52, A:M.54, H2O.1 MG.6: 5 residues within 4Å: Chain A: D.326, I.327, E.369, K.441 Ligands: GAV.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.326, A:I.327, A:E.369, A:E.369 MG.7: 3 residues within 4Å: Chain A: D.326, E.369, E.370 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.326, A:E.369 MG.12: 4 residues within 4Å: Chain B: D.9, D.52, M.54 Ligands: BEF.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.9, B:D.9, B:D.52, B:M.54, H2O.1 MG.16: 5 residues within 4Å: Chain B: D.326, I.327, E.369, K.441 Ligands: GAV.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.326, B:I.327, B:E.369, B:E.369

4 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.3: 10 residues within 4Å: Chain A: V.357, R.358, D.361, T.378, D.382, R.385, I.386, R.389 Chain B: R.312 Ligands: C2E.4 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.312, B:R.312, A:R.358, A:R.358, A:T.378, A:T.378, A:R.389, A:R.389 Salt bridges: A:R.358, A:D.361 pi-Cation interactions: A:R.358, A:R.358 C2E.4: 12 residues within 4Å: Chain A: S.355, N.356, V.357, R.358, A.359, R.389 Chain B: S.308, K.311, R.312, L.315, G.317 Ligands: C2E.3 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.308, B:R.312, B:R.312, B:R.312, B:G.317, A:R.358, A:A.359, A:R.389 Water bridges: B:L.315 Salt bridges: B:R.312 pi-Cation interactions: A:R.389, A:R.389 C2E.13: 9 residues within 4Å: Chain A: R.312 Chain B: R.358, D.361, T.378, D.382, R.385, I.386, R.389 Ligands: C2E.14 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.358, B:R.358, B:T.378, B:R.389, B:R.389, A:R.312, A:R.312 Salt bridges: B:R.358, B:D.361 pi-Cation interactions: B:R.358, B:R.358 C2E.14: 11 residues within 4Å: Chain A: S.308, K.311, R.312, L.315, G.317 Chain B: N.356, V.357, R.358, A.359, R.389 Ligands: C2E.13 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.358, B:A.359, A:S.308, A:R.312, A:R.312, A:R.312, A:G.317 pi-Cation interactions: B:R.389, B:R.389 Salt bridges: A:R.312

2 x GAV: GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE(Non-covalent)

GAV.5: 17 residues within 4Å: Chain A: D.326, I.327, D.328, F.329, F.330, K.331, N.334, H.339, G.342, D.343, L.346, R.365, G.368, E.369, K.441, R.445 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.329, A:F.330, A:K.331, A:N.334, A:N.334, A:R.365 Salt bridges: A:D.343, A:K.441, A:R.445 GAV.15: 19 residues within 4Å: Chain A: G.143, A.144 Chain B: D.326, I.327, D.328, F.329, F.330, K.331, N.334, H.339, G.342, D.343, L.346, R.365, G.368, E.369, K.441, R.445 Ligands: MG.16 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.329, B:F.330, B:K.331, B:N.334, B:N.334, B:R.365, B:R.365, A:A.144 Salt bridges: B:D.343, B:K.441, B:R.445

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: N.161, R.163, Q.164, R.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.161 Salt bridges: A:R.163, A:R.167 SO4.9: 4 residues within 4Å: Chain A: R.116, R.120 Chain B: R.116, R.120 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.120, A:R.116

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: A.418, A.420, A.452, A.453 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wassmann, P. et al., Structure of Bef3--Modified Response Regulator Pled: Implications for Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition. Structure (2007)

Release Date

2007-08-21

Peptides

RESPONSE REGULATOR PLED: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RESPONSE REGULATOR PLED

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