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The crystal structure of endo-arabinase from bacteroides thetaiotaomicron vpi-5482

Analyse The crystal structure of endo-arabinase from bacteroides thetaiotaomicron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C0P
Type: protein
Length: 284 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-arabinase
UniProt: Q8A6K8
Ligands: MG, CL
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endo-arabinase	protein	284	4% helix, 53% strand	Q8A6K8

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 4 copies · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

2 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	312	0.59	0.77	23	CL
2	134	0.46	0.77	22	TRS

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

5C0P · The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482 · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8A6K8
Elsewhere: RCSB PDB 5C0P · PDBe 5C0P · UniProt Q8A6K8

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