MolNFT v1 · #74300 · protein + DNA

Structure of REV1

3OSP · DNA repair protein REV1: “Structure of REV1”. X-ray diffraction, 2 ligands (DCP, MG), 6 pockets (best druggability 0.84). MolNFT v1 #74300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OSP
Type: protein + DNA
Length: 456 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein REV1; 5'-D(*TP*AP*AP*(3DR)P*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)- 3'…
EC: 2.7.7.-
UniProt: P12689
Ligands: DCP, MG
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein REV1 (EC 2.7.7.-)	protein	428	44% helix, 21% strand	P12689
T	5'-D(TPAPAP(3DR)PGPTPAPGPGPGPGPAPGPGPAPT)- 3'	dna	16	—	—
P	5'-D(APTPCPCPTPCPCPCPCPTPAP(DOC))-3'	dna	12	—	—

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P
MG · Magnesium ion · metal · 2 copies · chains A, P

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	1195	0.84	0.85	82	DCP, MG
2	401	0.71	0.83	41	empty
3	222	0.56	0.78	31	empty
4	55	0.51	0.88	14	empty
5	79	0.36	0.76	17	empty

Interfaces

3 interfaces between chains.

A–T · 1359 Å² buried · 32 hydrogen bonds · protein-nucleic
A–P · 613 Å² buried · 19 hydrogen bonds · protein-nucleic
T–P · 533 Å² buried · 55 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

3OSP · Structure of rev1 · the same entry in another collection · chain A against A, 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 3OSP · PDBe 3OSP · UniProt P12689

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