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Regulatory domain of aphb treated with cumene hydroperoxide from vibrio vulnificus

Analyse Regulatory domain of aphb treated with cumene hydroperoxide from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X0O
Type: protein
Length: 1,177 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysr family transcriptional regulator
UniProt: A0A087IWB4
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 31% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysr family transcriptional regulator	protein	194	31% helix, 31% strand	A0A087IWB4
B	Lysr family transcriptional regulator	protein	192	33% helix, 35% strand	A0A087IWB4
C	Lysr family transcriptional regulator	protein	199	30% helix, 35% strand	A0A087IWB4
D, E	Lysr family transcriptional regulator	protein	199	32% helix, 37% strand	A0A087IWB4
F	Lysr family transcriptional regulator	protein	194	31% helix, 35% strand	A0A087IWB4

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.81	0.82	92	empty
2	574	0.74	0.81	67	empty
3	282	0.71	0.85	33	empty
4	207	0.62	0.82	29	empty
5	553	0.59	0.73	42	empty

Interfaces

9 interfaces between chains.

A–B · 1479 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 1456 Å² buried · 21 hydrogen bonds · protein-protein
C–F · 1435 Å² buried · 21 hydrogen bonds · protein-protein
B–E · 321 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 191 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5X0O · Regulatory domain of AphB treated with Cumene hydroperoxide 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 A0A087IWB4
Elsewhere: RCSB PDB 5X0O · PDBe 5X0O · UniProt A0A087IWB4

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