SMTL ID : 5f7q.1

ROK repressor Lmo0178 from Listeria monocytogenes bound to operator

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.247, C.257, C.259, C.264 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.247, A:C.257, A:C.259, A:C.264 ZN.5: 4 residues within 4Å: Chain B: H.247, C.257, C.259, C.264 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.247, B:C.257, B:C.259, B:C.264 ZN.9: 4 residues within 4Å: Chain D: H.247, C.257, C.259, C.264 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.247, D:C.257, D:C.259, D:C.264 ZN.14: 4 residues within 4Å: Chain F: H.247, C.257, C.259, C.264 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.247, F:C.257, F:C.259, F:C.264

3 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.2: 4 residues within 4Å: Chain A: R.159, Y.191, L.388, Q.392 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.159, A:Q.392 Water bridges: A:D.193 PG5.6: 6 residues within 4Å: Chain B: R.159, Y.191, I.234, Y.236, L.388, Q.392 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.159, B:I.234, B:Y.236 PG5.10: 8 residues within 4Å: Chain D: R.159, Y.191, L.201, Q.233, I.234, Y.236, L.388, Q.392 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.159, D:I.234, D:Q.392 Water bridges: D:D.193

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 9 residues within 4Å: Chain A: V.157, N.158, I.165, A.238, Q.239, G.241 Chain B: N.332, F.362, F.367 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.158, A:N.158, B:N.332 Water bridges: A:R.159 PG4.4: 5 residues within 4Å: Chain A: E.29, K.210, Q.211, N.213, R.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.213 PG4.12: 13 residues within 4Å: Chain D: V.157, N.158, R.159, A.238, Q.239, G.240, G.241 Chain F: N.332, E.334, F.362, F.367, E.368, T.369 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:R.159, D:Q.239, F:N.332, F:E.334, F:T.369 Water bridges: F:E.334

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 10 residues within 4Å: Chain A: N.332, F.362 Chain B: V.157, N.158, R.159, I.165, A.238, Q.239, G.240, G.241 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.332, B:R.159, B:Q.239 Water bridges: B:A.242 PEG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.15: 6 residues within 4Å: Chain F: R.159, Y.191, Y.236, L.388, H.391, Q.392 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.159, F:Y.236, F:Q.392 Water bridges: F:H.391 PEG.16: 4 residues within 4Å: Chain F: R.28, E.29, N.106, L.206 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.30 PEG.17: 5 residues within 4Å: Chain F: E.29, K.210, Q.211, N.213, R.232 No protein-ligand interaction detected (PLIP) PEG.18: 2 residues within 4Å: Chain F: A.39, F.44 No protein-ligand interaction detected (PLIP)

2 x 7PE: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL(Non-functional Binders)

7PE.8: 14 residues within 4Å: Chain A: F.245, T.248, T.249, I.250, P.252, Y.322, N.326 Chain B: F.245, T.248, T.249, I.250, Y.322, G.323, N.326 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.248, B:N.326, A:N.326 Hydrophobic interactions: A:I.250 7PE.13: 15 residues within 4Å: Chain D: F.245, T.248, T.249, I.250, P.252, Y.322, G.323, N.326 Chain F: F.245, T.248, T.249, I.250, P.252, Y.322, N.326 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:N.326, F:T.248, F:N.326 Water bridges: D:Q.251, D:Y.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Light, S.H. et al., Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis. Nat Microbiol (2016)

Release Date

2016-09-07

Peptides

Lmo0178 protein: ABDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

D
J

F
L

Lmo0178 protein

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