SMTL ID : 4xrn.2 (1 other biounit)

Pilz domain with c-di-gmp of a protein from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 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: 17 residues within 4Å: Chain A: S.4, R.6, Q.7, R.10, D.33, L.34, S.35, G.37, G.38, F.39, A.40, R.76, R.84, G.86, C.87, E.88 Ligands: C2E.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.4, A:R.6, A:Q.7, A:R.10, A:S.35, A:S.35, A:R.84, A:R.84 Water bridges: A:F.8, A:R.10, A:R.76 Salt bridges: A:R.10, A:D.33, A:R.76 pi-Cation interactions: A:R.10 C2E.2: 8 residues within 4Å: Chain A: S.4, R.6, R.10, S.77, R.84 Ligands: C2E.1, C2E.3, ZN.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.4, A:S.4, A:R.6, A:R.10, A:R.10, A:S.77 Water bridges: A:R.6, A:R.6, A:R.6, A:R.6, A:R.6, A:R.76, A:R.84, A:R.84, A:R.84, A:R.84 Salt bridges: A:R.6, A:R.84 C2E.3: 4 residues within 4Å: Chain A: S.4 Ligands: C2E.2, ZN.4, ZN.5 No protein-ligand interaction detected (PLIP) C2E.9: 20 residues within 4Å: Chain B: S.4, Q.5, R.6, Q.7, R.10, D.33, L.34, S.35, G.37, G.38, F.39, A.40, R.76, R.84, G.86, C.87, E.88 Ligands: C2E.10, C2E.11, ZN.13 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.4, B:R.6, B:Q.7, B:R.10, B:S.35, B:S.35, B:R.84, B:R.84, B:C.87 Water bridges: B:Q.5, B:F.8, B:R.10, B:R.10, B:R.10, B:R.76, B:E.88 Salt bridges: B:R.10, B:D.33 pi-Cation interactions: B:R.10 C2E.10: 7 residues within 4Å: Chain B: R.6, R.10, R.76, S.77, R.84 Ligands: C2E.9, C2E.11 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.6, B:R.6, B:R.10, B:R.10, B:S.77 Water bridges: B:R.6, B:R.6, B:D.33, B:R.76, B:R.84, B:R.84, B:R.84 Salt bridges: B:R.6, B:R.84 pi-Cation interactions: B:R.6 C2E.11: 6 residues within 4Å: Chain B: G.3, S.4 Ligands: C2E.9, C2E.10, ZN.12, ZN.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.4, B:S.4, B:S.4

7 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.4: 1 residues within 4Å: Ligands: C2E.3 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Ligands: C2E.2, C2E.3 No protein-ligand interaction detected (PLIP) ZN.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Chain A: D.79 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, H2O.3, H2O.3 ZN.8: 1 residues within 4Å: Chain A: D.28 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.28, H2O.3, H2O.3 ZN.12: 2 residues within 4Å: Chain B: S.4 Ligands: C2E.11 No protein-ligand interaction detected (PLIP) ZN.13: 2 residues within 4Å: Ligands: C2E.9, C2E.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, K.K. et al., Pilz domain with c-di-gmp of a protein from Pseudomonas aeruginosa. To Be Published

Release Date

2016-02-03

Peptides

Alginate biosynthesis protein Alg44: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Alginate biosynthesis protein Alg44

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