Research workbench

Regulatory domain of variant C227S aphb from vibrio vulnificus

Analyse Regulatory domain of variant C227S aphb from vibrio vulnificus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X0N
Type: protein
Length: 1,147 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysr family transcriptional regulator
UniProt: A0A087IWB4
Pockets: 11 · best druggability 0.67

Structure

x-ray diffraction · 6 distinct chains · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysr family transcriptional regulator	protein	186	26% helix, 34% strand	A0A087IWB4
B	Lysr family transcriptional regulator	protein	190	28% helix, 34% strand	A0A087IWB4
C	Lysr family transcriptional regulator	protein	196	29% helix, 31% strand	A0A087IWB4
D	Lysr family transcriptional regulator	protein	197	30% helix, 31% strand	A0A087IWB4
E	Lysr family transcriptional regulator	protein	197	27% helix, 32% strand	A0A087IWB4
F	Lysr family transcriptional regulator	protein	181	29% helix, 35% strand	A0A087IWB4

Pockets

11 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	185	0.67	0.86	25	empty
2	224	0.66	0.84	32	empty
3	445	0.61	0.76	57	empty
4	428	0.59	0.75	52	empty
5	220	0.56	0.79	26	empty

Interfaces

5 interfaces between chains.

E–F · 1508 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 1503 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1458 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 951 Å² buried · 15 hydrogen bonds · protein-protein
B–E · 948 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5X0N · Regulatory domain of variant C227S AphB 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 5X0N · PDBe 5X0N · UniProt A0A087IWB4

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