SMTL ID : 6ij2.2 (1 other biounit)

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x G- G: RNA (5'-R(P*GP*G)-3')(Non-covalent)

G-G.1: 24 residues within 4Å: Chain A: 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, E.215, G.216, V.217, E.218, G.236, Y.237, P.242 Ligands: CA.3, CA.4, CA.6 Protein-ligand interaction information (PLIP) not available G-G.2: 23 residues within 4Å: Chain B: 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, E.215, G.216, V.217, E.218, G.236, Y.237, P.242 Ligands: CA.7, CA.8, CA.10 Protein-ligand interaction information (PLIP) not available

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.158, D.159, E.215 Ligands: G-G.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.158, A:D.159, A:E.215, A:E.215, H2O.2 CA.4: 5 residues within 4Å: Chain A: E.45, N.95, E.128, D.158 Ligands: G-G.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.45, A:E.128, A:D.158, A:D.158, H2O.1 CA.5: 4 residues within 4Å: Chain A: D.159, S.162, Y.164, G.166 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.159, A:S.162, A:Y.164, H2O.3, H2O.5 CA.6: 5 residues within 4Å: Chain A: T.130, D.158, D.159 Ligands: G-G.1, G-G.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.130, A:D.158, A:D.159, A:D.159, H2O.7 CA.7: 5 residues within 4Å: Chain B: E.45, N.95, E.128, D.158 Ligands: G-G.2 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.45, B:E.128, B:D.158, B:D.158, H2O.9 CA.8: 4 residues within 4Å: Chain B: D.158, D.159, E.215 Ligands: G-G.2 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.158, B:D.158, B:D.159, B:E.215, H2O.8 CA.9: 4 residues within 4Å: Chain B: D.159, S.162, G.163, Y.164 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.159, B:S.162, B:Y.164, H2O.9, H2O.11 CA.10: 4 residues within 4Å: Chain B: T.130, D.158, D.159 Ligands: G-G.2 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.130, B:D.159, B:D.159, H2O.11, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, M. et al., Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication. Biochem.J. (2019)

Release Date

2019-10-09

Peptides

EAL domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

EAL domain protein

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