MolNFT v1 · #169282 · protein + DNA

REV1 MG2+-facilitated product complex with one monophosphate

6X73 · DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*C)-3'): “REV1 MG2+-facilitated product complex with one monophosphate”. X-ray diffraction, 3 ligands (MG, PO4, NH4), 5 pockets (best druggability 0.83). MolNFT v1 #169282 on GenesisL1…

PDB: 6X73
Type: protein + DNA
Length: 468 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*C)-3'); DNA (5'…
EC: 2.7.7.-
UniProt: P12689
Ligands: MG, PO4, NH4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAPGP*C)-3')	dna	13	—	—
T	DNA (5'- D(CPAPTPCPGPCPTPAPCPCPAPCPAPCPCPCP*C)-3')	dna	16	—	—
A	DNA repair protein REV1 (EC 2.7.7.-)	protein	439	43% helix, 19% strand	P12689

Ligands and binding sites

MG · Magnesium ion · metal · chains P, A
PO4 · Phosphate ion · ion · chains P, A
NH4 · Ammonium ion · ion · chains P, A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1089	0.83	0.84	80	empty
2	1020	0.79	0.81	72	PO4, NH4
3	174	0.58	0.81	25	empty
4	71	0.41	0.79	16	empty
5	69	0.34	0.76	16	empty

Interfaces

3 interfaces between chains.

T–A · 1372 Å² buried · 40 hydrogen bonds · protein-nucleic
P–A · 819 Å² buried · 30 hydrogen bonds · protein-nucleic
P–T · 548 Å² buried · 58 hydrogen bonds · nucleic-nucleic

Compared structures

6X73 · Rev1 Mg2+-facilitated Product Complex with one monophosphate · the same entry in another collection · chain P against P, TM-score 1.00
P12689 · AlphaFold monomer V2.0 prediction for DNA repair protein REV1 (P12689) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P12689
Elsewhere: RCSB PDB 6X73 · PDBe 6X73 · UniProt P12689

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.