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Ternary complex of the catalytic core of REV1 with DNA and dctp.

Analyse Ternary complex of the catalytic core of REV1 with DNA and dctp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2AQ4
Type: protein + DNA
Length: 456 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*C)-3'; 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP…
EC: 2.7.7.-
UniProt: P12689
Ligands: DCP, MG
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	5'-D(APTPCPCPTPCPCPCPCPTPAPC)-3'	dna	12	—	—
T	5'-D(TPAPAPGPGPTPAPGPGPGPGPAPGPGPAPT)-3'	dna	16	—	—
A	DNA repair protein REV1 (EC 2.7.7.-)	protein	428	43% helix, 20% strand	P12689

Ligands and binding sites

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

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	756	0.83	0.87	47	empty
2	1000	0.78	0.80	73	MG, DCP
3	106	0.57	0.85	25	empty
4	192	0.54	0.78	31	empty
5	59	0.35	0.78	17	empty

Interfaces

3 interfaces between chains.

T–A · 1468 Å² buried · 36 hydrogen bonds · protein-nucleic
P–A · 596 Å² buried · 19 hydrogen bonds · protein-nucleic
P–T · 528 Å² buried · 44 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2AQ4 · Ternary complex of the catalytic core of REV1 with DNA and dCTP. · 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 2AQ4 · PDBe 2AQ4 · UniProt P12689

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