MolNFT v1 · #114254 · protein

OXYR2 E204G regulatory domain from vibrio vulnificus

5B70 · Lysr family transcriptional regulator: “OXYR2 E204G regulatory domain from vibrio vulnificus”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #114254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B70
Type: protein
Length: 848 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysr family transcriptional regulator
UniProt: A0A087I947
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysr family transcriptional regulator	protein	209	33% helix, 27% strand	A0A087I947
B	Lysr family transcriptional regulator	protein	214	31% helix, 29% strand	A0A087I947
C	Lysr family transcriptional regulator	protein	211	33% helix, 27% strand	A0A087I947
D	Lysr family transcriptional regulator	protein	214	31% helix, 26% strand	A0A087I947

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains C, D

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	804	0.75	0.79	69	empty
2	247	0.62	0.81	27	empty
3	116	0.59	0.86	25	empty
4	160	0.55	0.81	32	empty
5	60	0.31	0.75	13	empty

Interfaces

4 interfaces between chains.

A–D · 1812 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 1812 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 326 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 130 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5B70 · OxyR2 E204G regulatory domain from Vibrio vulnificus · the same entry in another collection · chain A against A, 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 A0A087I947
Elsewhere: RCSB PDB 5B70 · PDBe 5B70 · UniProt A0A087I947

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