SMTL ID : 6pwk.1

Vibrio cholerae LapD S helix-GGDEF-EAL (bound to c-di-GMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

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.1: 22 residues within 4Å: Chain A: R.203, Q.205, E.218, F.220, S.221, T.231, A.232, N.233, L.236, F.248, D.249, V.252, N.272, I.273, A.274, D.334, R.391, V.392, E.393, G.411, F.412 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.203, A:R.203, A:Q.205, A:S.221, A:N.272, A:N.272, A:A.274, A:F.412 Water bridges: A:A.232, A:A.232, A:N.272, A:N.272, A:R.391 Salt bridges: A:R.203, A:D.249, A:R.391, A:E.393 pi-Stacking: A:F.412, A:F.412 C2E.2: 12 residues within 4Å: Chain A: R.28, I.49, E.96, T.149, L.152, S.153, D.156, G.183, K.184, Q.185 Chain B: Y.64, D.68 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.28, A:R.28, A:E.96, A:D.156, A:K.184, A:K.184, A:Q.185, A:Q.185 Salt bridges: A:E.96, A:D.156, B:D.68 pi-Stacking: B:Y.64 C2E.4: 22 residues within 4Å: Chain B: R.203, Q.205, E.218, F.220, S.221, T.231, A.232, N.233, L.236, F.248, D.249, V.252, N.272, I.273, A.274, D.334, R.391, V.392, E.393, G.411, F.412 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.203, B:Q.205, B:S.221, B:N.233, B:N.272, B:N.272, B:A.274, B:F.412 Water bridges: B:N.272, B:N.272, B:E.304 Salt bridges: B:R.203, B:D.249, B:R.391, B:E.393 pi-Stacking: B:F.412 C2E.5: 13 residues within 4Å: Chain A: Y.64, D.68 Chain B: R.28, I.49, E.96, T.149, L.152, S.153, D.156, L.159, G.183, K.184, Q.185 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.28, B:R.28, B:E.96, B:K.184, B:K.184, B:Q.185 Salt bridges: B:E.96, B:D.156, A:D.68 pi-Stacking: A:Y.64

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.218, N.272, E.304, D.334 Ligands: C2E.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.218, A:E.304, A:D.334, A:D.334, C2E.1 MG.6: 5 residues within 4Å: Chain B: E.218, N.272, E.304, D.334 Ligands: C2E.4 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.218, B:E.304, B:D.334, H2O.1, C2E.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitts, G. et al., A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae. Mbio (2019)

Release Date

2019-10-09

Peptides

GGDEF and EAL domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GGDEF and EAL domain-containing protein

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