SMTL ID : 6k6t.2 (1 other biounit)

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x C2I: 9-[(1R,6R,8R,9S,10R,15S,17R,18S)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-17-(6-oxidanylidene-3H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-3H-purin-6-one(Non-covalent)

C2I.1: 21 residues within 4Å: Chain A: Q.31, E.45, L.47, V.48, R.49, A.56, I.60, C.75, N.95, L.97, D.158, D.159, M.182, G.216, V.217, E.218, G.236, Y.237, P.242 Ligands: CA.2, CA.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.31, A:Q.31, A:V.48, A:N.95, A:R.186, A:E.218, A:Y.237 Water bridges: A:A.56 Salt bridges: A:R.49 pi-Stacking: A:Y.237 C2I.4: 24 residues within 4Å: Chain B: M.28, Q.31, E.45, L.47, V.48, R.49, A.56, I.60, C.75, N.95, L.97, D.158, D.159, M.182, R.186, E.215, G.216, V.217, E.218, G.236, Y.237, P.242 Ligands: CA.5, CA.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.31, B:Q.31, B:V.48, B:R.186, B:E.218, B:Y.237 Water bridges: B:A.56, B:A.56, B:N.95, B:Y.164 Salt bridges: B:R.49 pi-Stacking: B:Y.237, B:Y.237

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.45, N.95, E.128, D.158 Ligands: C2I.1, CA.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.45, A:E.128, A:D.158, H2O.1, C2I.1 CA.3: 5 residues within 4Å: Chain A: D.158, D.159, E.215 Ligands: C2I.1, CA.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.158, A:D.159, A:E.215, H2O.1, C2I.1 CA.5: 6 residues within 4Å: Chain B: E.45, N.95, E.128, D.158 Ligands: C2I.4, CA.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.45, B:E.128, B:D.158, C2I.4, H2O.5 CA.6: 5 residues within 4Å: Chain B: D.158, D.159, E.215 Ligands: C2I.4, CA.5 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.158, B:D.159, B:E.215, C2I.4, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, M. et al., Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form. To Be Published

Release Date

2020-06-17

Peptides

EAL domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

EAL domain protein

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