MolNFT v1 · #145694 · protein + DNA

Human aprataxin (aptx) R199H bound to RNA-DNA, AMP and zn product complex

6CVP: “Human aprataxin (aptx) R199H bound to RNA-DNA, AMP and zn product complex”. X-ray diffraction, 3 ligands (AMP, ZN, NA), 6 pockets (best druggability 0.66). MolNFT v1 #145694 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6CVP
Type: protein + DNA
Length: 395 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aprataxin; DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'); DNA…
EC: 3.1.11.7, 3.1.12.2
UniProt: Q7Z2E3
Ligands: AMP, ZN, NA
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aprataxin (EC 3.1.11.7, 3.1.12.2)	protein	176	41% helix, 19% strand	Q7Z2E3
D, G	DNA/RNA (5'-R(PG)-D(PTPTPAPTPGPAPTPTPC)-3')	dna	10	—	—
E, H	DNA (5'-D(GPAPAPTPCPAPTPAPAPC)-3')	dna	10	—	—
B	Aprataxin (EC 3.1.11.7, 3.1.12.2)	protein	179	42% helix, 18% strand	Q7Z2E3

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, D, B, G
ZN · Zinc ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · chains B, G

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	152	0.66	0.87	26	AMP
2	183	0.64	0.84	30	AMP
3	374	0.59	0.76	30	empty
4	384	0.57	0.75	28	NA
5	65	0.34	0.77	17	empty

Interfaces

8 interfaces between chains.

D–E · 404 Å² buried · 31 hydrogen bonds · nucleic-nucleic
G–H · 402 Å² buried · 31 hydrogen bonds · nucleic-nucleic
A–D · 369 Å² buried · 6 hydrogen bonds · protein-nucleic
B–G · 348 Å² buried · 5 hydrogen bonds · protein-nucleic
A–E · 173 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

6CVP · Human Aprataxin (Aptx) R199H bound to RNA-DNA, AMP and Zn product complex · the same entry in another collection · chain H against H, TM-score 1.00
Q7Z2E3 · AlphaFold monomer V2.0 prediction for aprataxin (Q7Z2E3) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q7Z2E3
Elsewhere: RCSB PDB 6CVP · PDBe 6CVP · UniProt Q7Z2E3

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