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Crystal structure of a beta-helix domain retrieved from capybara gut metagenome

Analyse Crystal structure of a beta-helix domain retrieved from capybara gut metagenome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JVI
Type: protein
Length: 842 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.85
Source: metagenome
Molecule: Beta-helix domain
Ligands: CA
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · resolution 1.85 · 1 distinct chain · 6% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-helix domain	protein	421	6% helix, 43% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

4 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	390	0.64	0.78	41	empty
2	70	0.34	0.76	17	empty
3	57	0.28	0.74	15	empty
4	56	0.27	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 510 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7JVI · Crystal structure of a beta-helix domain retrieved from capybara gut metagenome · 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
Elsewhere: RCSB PDB 7JVI · PDBe 7JVI

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