SMTL ID : 7b0e.1

Crystal structure of SmbA loop deletion mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 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: 14 residues within 4Å: Chain A: R.76, R.78, D.80, A.81, N.111, D.112, Q.114, A.141, S.142, R.143, S.160, S.161, P.162, E.188 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.76, A:R.78, A:D.80, A:D.80, A:A.81, A:N.111, A:D.112, A:Q.114, A:S.142, A:S.142, A:R.143, A:R.143, A:R.143 Water bridges: A:R.78, A:R.143, A:E.188, A:E.188, A:R.233, A:R.233 Salt bridges: A:E.188 pi-Cation interactions: A:R.143, A:R.143

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 1 residues within 4Å: Chain A: E.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.262 EDO.3: 6 residues within 4Å: Chain A: Y.222, T.225, C.258, I.261, E.262 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.225, A:E.262, A:E.262 EDO.4: 2 residues within 4Å: Chain A: N.182, F.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.182 Water bridges: A:S.8 EDO.5: 5 residues within 4Å: Chain A: Y.163, Y.222, T.225, E.226 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.225 EDO.6: 6 residues within 4Å: Chain A: M.120, E.123, S.124, Q.127 Ligands: EDO.7, CA.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.127, A:Q.127 EDO.7: 4 residues within 4Å: Chain A: S.124, Q.127 Ligands: EDO.6, CA.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.124, A:Q.127 EDO.8: 6 residues within 4Å: Chain A: T.9, V.11, F.72, D.106, R.136 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.106 EDO.9: 7 residues within 4Å: Chain A: D.112, Q.114, S.115, D.145, I.146, D.147 Ligands: CA.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.112, A:D.147 Water bridges: A:S.115, A:D.145 EDO.10: 4 residues within 4Å: Chain A: R.143, A.170, E.171, R.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.171, A:R.174, A:R.174 EDO.11: 9 residues within 4Å: Chain A: V.11, A.12, N.44, H.69, L.70, L.71, F.72, D.106 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.44, A:L.70 Water bridges: A:A.12 EDO.12: 7 residues within 4Å: Chain A: L.26, D.30, A.33, L.34, D.237, N.238, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.30 Water bridges: A:R.239, A:R.239 EDO.13: 10 residues within 4Å: Chain A: V.140, S.142, G.144, I.146, V.159, S.160, S.161, R.174, I.175, A.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.160 Water bridges: A:I.146, A:R.174

2 x NA: SODIUM ION(Non-functional Binders)

NA.14: 6 residues within 4Å: Chain A: Q.47, L.109, S.160, I.186, E.188, R.233 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.47, A:S.160, A:R.233, A:R.233 NA.15: 4 residues within 4Å: Chain A: R.19, R.233, V.234, T.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.233, A:R.233, A:T.235 Water bridges: A:D.189

3 x CA: CALCIUM ION(Non-covalent)

CA.16: 3 residues within 4Å: Chain A: Q.127 Ligands: EDO.6, EDO.7 No protein-ligand interaction detected (PLIP) CA.17: 2 residues within 4Å: Chain A: D.22, D.51 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.22, A:D.51, H2O.9 CA.18: 4 residues within 4Å: Chain A: D.112, Q.114, D.145 Ligands: EDO.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.112, A:D.145, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubey, B.N. et al., High-resolution crystal structure of loop deletion mutant SmbA bound to a monomeric c-di-GMP. To Be Published

Release Date

2021-12-01

Peptides

SmbA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SmbA