Research workbench

Xpf from aeropyrum pernix

Analyse Xpf from aeropyrum pernix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BHN
Type: protein
Length: 815 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xpf endonuclease
EC: 2.7.7.-
UniProt: Q9YC15
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Xpf endonuclease (EC 2.7.7.-)	protein	211	50% helix, 15% strand	Q9YC15
B	Xpf endonuclease (EC 2.7.7.-)	protein	199	51% helix, 15% strand	Q9YC15
C	Xpf endonuclease (EC 2.7.7.-)	protein	194	51% helix, 16% strand	Q9YC15

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	554	0.68	0.78	51	empty
2	70	0.62	0.90	21	empty
3	108	0.40	0.76	21	empty
4	103	0.36	0.74	16	empty
5	86	0.32	0.73	16	empty

Interfaces

3 interfaces between chains.

A–B · 2611 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2336 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 143 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2BHN · XPF from Aeropyrum pernix · 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 Q9YC15
Elsewhere: RCSB PDB 2BHN · PDBe 2BHN · UniProt Q9YC15

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