Research workbench

APLF/XRCC4 complex

Analyse APLF/XRCC4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E50
Type: protein
Length: 234 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aprataxin and pnk-like factor; XRCC4
EC: 4.2.99.18
UniProt: Q8IW19
Ligands: MG
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aprataxin and pnk-like factor (EC 4.2.99.18)	protein	110	0% helix, 46% strand	Q8IW19
C, D	XRCC4	protein	7	0% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, C, B, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.34	0.75	17	empty
2	94	0.34	0.73	18	empty

Interfaces

5 interfaces between chains.

A–B · 827 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 518 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 491 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 52 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 49 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

5E50 · APLF/XRCC4 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q8IW19 · AlphaFold monomer V2.0 prediction for aprataxin and pnk-like factor (Q8IW19) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q8IW19
Elsewhere: RCSB PDB 5E50 · PDBe 5E50 · UniProt Q8IW19

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