Research workbench

Rok repressor LMO0178 from listeria monocytogenes bound to operator

Analyse Rok repressor LMO0178 from listeria monocytogenes bound to operator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F7Q
Type: protein + DNA
Length: 1,621 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LMO0178 protein; Operator
UniProt: Q8YAF1
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	LMO0178 protein	protein	385	41% helix, 24% strand	Q8YAF1
E, J	LMO0178 protein	protein	396	43% helix, 23% strand	Q8YAF1
F	Operator	dna	29	—	—
K	Operator	dna	29	—	—
L	LMO0178 protein	protein	386	42% helix, 24% strand	Q8YAF1

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains C, E, J, L
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains C, E, L
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 3 copies · chains C, E, J
PG4 · Tetraethylene glycol · additive · 3 copies · chains C, E, J, L
7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · 2 copies · chains C, E, J, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	852	0.81	0.83	87	PG5, PEG
2	1155	0.76	0.78	83	PG5
3	397	0.74	0.85	50	empty
4	438	0.73	0.83	51	empty
5	338	0.71	0.84	43	empty

Interfaces

11 interfaces between chains.

J–L · 2256 Å² buried · 30 hydrogen bonds · protein-protein
C–E · 2231 Å² buried · 32 hydrogen bonds · protein-protein
F–K · 1242 Å² buried · 97 hydrogen bonds · nucleic-nucleic
C–F · 695 Å² buried · 10 hydrogen bonds · protein-nucleic
K–L · 685 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

5F7Q · ROK repressor Lmo0178 from Listeria monocytogenes bound to operator · the same entry in another collection · chain C against C, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8YAF1
Elsewhere: RCSB PDB 5F7Q · PDBe 5F7Q · UniProt Q8YAF1

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