SMTL ID : 6p7o.1

Structure of E. coli MS115-1 NucC, Apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.73, E.104, A.105, K.106 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.73, A:E.104, A:A.105, H2O.1, H2O.1, H2O.5 MG.5: 4 residues within 4Å: Chain B: D.73, E.104, A.105, K.106 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.73, B:E.104, B:A.105, H2O.8, H2O.8, H2O.12 MG.9: 4 residues within 4Å: Chain C: D.73, E.104, A.105, K.106 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.73, C:E.104, C:A.105, H2O.15, H2O.15, H2O.18

3 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 12 residues within 4Å: Chain A: Q.55, A.57, F.77, F.84, I.85, K.87, I.92 Chain C: T.48, Y.49, L.50, P.51, K.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.55, A:K.87 Water bridges: A:I.85 P6G.6: 12 residues within 4Å: Chain A: T.48, Y.49, L.50, P.51, K.52 Chain B: Q.55, A.57, F.77, F.84, I.85, K.87, I.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.55, B:K.87 Water bridges: B:I.85 P6G.10: 12 residues within 4Å: Chain B: T.48, Y.49, L.50, P.51, K.52 Chain C: Q.55, A.57, F.77, F.84, I.85, K.87, I.92 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.55, C:K.87 Water bridges: C:I.85

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 12 residues within 4Å: Chain A: R.125, P.148, I.149, L.150, L.176, S.177, D.178, R.180, D.182, N.196, Q.220 Ligands: CL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.125, A:S.177, A:R.180 Water bridges: A:R.180, A:N.196 PGE.7: 12 residues within 4Å: Chain B: R.125, P.148, I.149, L.150, L.176, S.177, D.178, R.180, D.182, N.196, Q.220 Ligands: CL.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.125, B:S.177, B:R.180 Water bridges: B:R.180, B:N.196 PGE.11: 12 residues within 4Å: Chain C: R.125, P.148, I.149, L.150, L.176, S.177, D.178, R.180, D.182, N.196, Q.220 Ligands: CL.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.125, C:S.177, C:R.180 Water bridges: C:R.180, C:N.196

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: R.125, R.129, P.148, I.149 Ligands: PGE.3 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: R.125, R.129, P.148, I.149 Ligands: PGE.7 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: R.125, R.129, P.148, I.149 Ligands: PGE.11 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lau, R.K. et al., Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity. Mol.Cell (2020)

Release Date

2019-12-25

Peptides

E. coli MS115-1 NucC: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

E. coli MS115-1 NucC