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VCAM4I restriction endonuclease in the absence of DNA

Analyse VCAM4I restriction endonuclease in the absence of DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YEX
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hnh endonuclease
UniProt: A0A344KQF3
Ligands: CL, SO4
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hnh endonuclease	protein	309	38% helix, 19% strand	A0A344KQF3
B	Hnh endonuclease	protein	303	39% helix, 18% strand	A0A344KQF3

Ligands and binding sites

CL · Chloride ion · ion · 12 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B

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

Pockets

6 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	1069	0.83	0.84	89	empty
2	139	0.39	0.73	19	empty
3	121	0.38	0.74	24	empty
4	69	0.35	0.77	14	empty
5	64	0.34	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 2297 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

6YEX · VcaM4I restriction endonuclease in the absence of DNA · 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 A0A344KQF3
Elsewhere: RCSB PDB 6YEX · PDBe 6YEX · UniProt A0A344KQF3

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