MolNFT v1 · #165422 · protein + DNA

Human xpg-DNA, complex 2

6TUX · DNA repair protein complementing xp-G CELLS,DNA repair…: “Human xpg-DNA, complex 2”. X-ray diffraction, 14 pockets (best druggability 0.73). MolNFT v1 #165422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6TUX
Type: protein + DNA
Length: 675 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein complementing xp-G CELLS,DNA repair protein complementing xp-G cells…
EC: 3.1.-.-
UniProt: P28715
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 6 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein complementing xp-G CELLS,DNA repair protein complementing xp-G cells (EC 3.1.-.-)	protein	330	48% helix, 10% strand	P28715
B	DNA repair protein complementing xp-G CELLS,DNA repair protein complementing xp-G cells (EC 3.1.-.-)	protein	315	53% helix, 10% strand	P28715
C	DNA (5'-D(PGPCPAPGPAPGPTPT)-3')	dna	8	—	—
D	DNA (5'-D(PAPAPCPTPCPTPGPC)-3')	dna	8	—	—
E	DNA (5'-D(PGPCPAPGPAPGPTPT)-3')	dna	7	—	—
F	DNA (5'-D(PAPAPCPTPCPTPGPC)-3')	dna	7	—	—

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	915	0.73	0.77	87	empty
2	269	0.60	0.79	30	empty
3	382	0.59	0.76	38	empty
4	286	0.58	0.78	38	empty
5	130	0.58	0.83	21	empty

Interfaces

7 interfaces between chains.

A–B · 577 Å² buried · 1 hydrogen bond · protein-protein
C–D · 368 Å² buried · 23 hydrogen bonds · nucleic-nucleic
E–F · 292 Å² buried · 16 hydrogen bonds · nucleic-nucleic
A–D · 229 Å² buried · 6 hydrogen bonds · protein-nucleic
B–F · 200 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

6TUX · human XPG-DNA, Complex 2 · the same entry in another collection · chain F against F, TM-score 1.00
P28715 · AlphaFold monomer V2.0 prediction for DNA repair protein complementing xp-G cells (P28715) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P28715
Elsewhere: RCSB PDB 6TUX · PDBe 6TUX · UniProt P28715

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