MolNFT v1 · #169284 · protein + DNA

REV1 MN2+-facilitated product complex with second dctp bound

6X75 · DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*C)-3'): “REV1 MN2+-facilitated product complex with second dctp bound”. X-ray diffraction, 2 ligands (DCP, MN), 5 pockets (best druggability 0.84). MolNFT v1 #169284 on GenesisL1: 3D…

PDB: 6X75
Type: protein + DNA
Length: 467 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: DCP, MN
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 20% 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	438	44% helix, 20% strand	P12689

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, A
MN · Manganese (II) ion · metal · 4 copies · chains P, A
GOL · Glycerol · additive · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	942	0.84	0.86	72	empty
2	1042	0.79	0.81	77	MN, DCP
3	92	0.48	0.81	16	GOL
4	60	0.42	0.81	16	empty
5	70	0.36	0.77	16	empty

Interfaces

3 interfaces between chains.

T–A · 1385 Å² buried · 36 hydrogen bonds · protein-nucleic
P–A · 701 Å² buried · 24 hydrogen bonds · protein-nucleic
P–T · 556 Å² buried · 54 hydrogen bonds · nucleic-nucleic

Compared structures

6X75 · Rev1 Mn2+-facilitated Product Complex with second dCTP bound · 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 6X75 · PDBe 6X75 · UniProt P12689

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