SMTL ID : 2wb4.1

activated diguanylate cyclase PleD in complex with c-di-GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.1: 7 residues within 4Å: Chain A: D.53, V.54, M.55, T.83, A.84, K.105 Ligands: MG.2 No protein-ligand interaction detected (PLIP) BEF.7: 7 residues within 4Å: Chain B: D.53, V.54, M.55, T.83, A.84, K.105 Ligands: MG.8 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.10, D.53, M.55 Ligands: BEF.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.53, A:M.55, H2O.1 MG.8: 4 residues within 4Å: Chain B: D.10, D.53, M.55 Ligands: BEF.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.53, B:M.55, H2O.1, H2O.2 MG.12: 5 residues within 4Å: Chain B: G.368, G.369, E.370, E.371 Ligands: C2E.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.371

5 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.358, R.359, D.362, T.379, D.383, R.386, I.387, R.390 Chain B: R.313 Ligands: C2E.4 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.359, A:R.359, A:T.379, A:T.379, A:R.390, A:R.390, B:R.313, B:R.313 Water bridges: A:R.359, A:R.359 Salt bridges: A:R.359, A:D.362 pi-Cation interactions: A:R.359, A:R.359 C2E.4: 12 residues within 4Å: Chain A: S.356, N.357, V.358, R.359, A.360, R.390 Chain B: S.309, K.312, R.313, L.316, G.317 Ligands: C2E.3 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.309, B:K.312, B:R.313, B:R.313, B:R.313, B:L.316, A:R.359, A:A.360, A:R.390 Salt bridges: B:R.313 Water bridges: A:R.390 pi-Cation interactions: A:R.390 C2E.9: 10 residues within 4Å: Chain A: R.313 Chain B: V.358, R.359, D.362, T.379, D.383, R.386, I.387, R.390 Ligands: C2E.10 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.359, B:R.359, B:T.379, B:R.390, B:R.390, A:R.313, A:R.313 Salt bridges: B:R.359, B:D.362 pi-Cation interactions: B:R.359, B:R.359 C2E.10: 12 residues within 4Å: Chain A: S.309, K.312, R.313, L.316, G.317 Chain B: S.356, N.357, V.358, R.359, A.360, R.390 Ligands: C2E.9 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.359, B:A.360, B:R.390, B:R.390, A:S.309, A:K.312, A:R.313, A:R.313, A:R.313 pi-Cation interactions: B:R.390 Water bridges: A:G.317 Salt bridges: A:R.313 C2E.11: 17 residues within 4Å: Chain A: P.72, R.137, G.144, A.145, A.146, A.147, Y.277 Chain B: F.331, N.335, H.340, G.343, D.344, R.366, G.369, E.370, E.371 Ligands: MG.12 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.335, B:N.335, B:R.366, B:G.369, A:A.146 Salt bridges: B:K.332, B:D.344, A:E.133 Water bridges: A:R.75, A:R.75 pi-Cation interactions: A:R.137

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

SO4.5: 4 residues within 4Å: Chain A: R.117, R.121 Chain B: R.117, R.121 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.117, B:R.121, A:R.117, A:R.121 SO4.6: 7 residues within 4Å: Chain A: D.327, I.328, D.329, F.330, E.370, K.442, R.446 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.330, A:E.370 Water bridges: A:F.331 Salt bridges: A:K.442, A:R.446 SO4.13: 8 residues within 4Å: Chain B: D.327, I.328, D.329, F.330, F.331, E.370, K.442, R.446 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.327, B:F.330, B:F.331 Water bridges: B:F.330, B:K.332 Salt bridges: B:K.442, B:R.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wassmann, P. et al., Crystal Structure of Activated Pled, Identification of Dimerization and Catalysis Relevant Regulatory Mechanisms. To be Published

Release Date

2010-04-21

Peptides

DIGUANYLATE CYCLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DIGUANYLATE CYCLASE