Research workbench

DNA repair helicase HEL308

Analyse DNA repair helicase HEL308 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VA8
Type: protein
Length: 1,388 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SKI2-type helicase
Ligands: SO4
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SKI2-type helicase	protein	693	54% helix, 12% strand	—
B	SKI2-type helicase	protein	695	54% helix, 13% strand	—

Ligands and binding sites

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

15 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	851	0.76	0.80	97	SO4
2	865	0.74	0.78	59	empty
3	752	0.74	0.79	69	SO4
4	840	0.73	0.78	60	empty
5	567	0.70	0.79	64	empty

Interfaces

1 interface between chains.

A–B · 1243 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2VA8 · DNA Repair Helicase Hel308 · 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 2VA8 · PDBe 2VA8

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