MolNFT v1 · #116473 · protein

Crystal structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with L-arabinose

5DEQ · Transcriptional regulator arar: “Crystal structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with…”. X-ray diffraction, 2 ligands (ARA, SO4), 3 pockets (best druggability 0.75). MolNFT v1…

PDB: 5DEQ
Type: protein
Length: 437 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator arar
UniProt: Q8AAV8
Ligands: ARA, SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator arar	protein	214	30% helix, 29% strand	Q8AAV8
B	Transcriptional regulator arar	protein	223	28% helix, 28% strand	Q8AAV8

Ligands and binding sites

ARA · alpha-L-arabinopyranose · sugar · 2 copies · chains A, B
SO4 · Sulfate ion · ion
FMT · Formic acid · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1062	0.75	0.77	96	FMT
2	111	0.38	0.74	21	empty
3	62	0.31	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 2027 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 modified (engineered).

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 Q8AAV8
Elsewhere: RCSB PDB 5DEQ · PDBe 5DEQ · UniProt Q8AAV8

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