MolNFT v1 · #169278 · protein + DNA

REV1 ternary complex with dctp and CA2+

6X6Z · DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3'): “REV1 ternary complex with dctp and CA2+”. X-ray diffraction, 2 ligands (DCP, CA), 5 pockets (best druggability 0.84). MolNFT v1 #169278 on GenesisL1: 3D structure, binding sites…

PDB: 6X6Z
Type: protein + DNA
Length: 466 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*G)-3'); DNA (5'…
EC: 2.7.7.-
UniProt: P12689
Ligands: DCP, CA
Pockets: 5 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAPG)-3')	dna	12	—	—
T	DNA (5'- D(CPAPTPCPGPCPTPAPCPCPAPCPAPCPCPCP*C)-3')	dna	16	—	—
A	DNA repair protein REV1 (EC 2.7.7.-)	protein	438	43% helix, 20% strand	P12689

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, A
CA · Calcium ion · metal · 3 copies · chains P, A
GOL · Glycerol · additive · chains P, T, 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	1030	0.84	0.85	77	empty
2	1085	0.80	0.82	77	DCP, GOL, CA
3	194	0.55	0.79	24	empty
4	66	0.44	0.82	18	empty
5	67	0.33	0.75	16	empty

Interfaces

3 interfaces between chains.

T–A · 1384 Å² buried · 36 hydrogen bonds · protein-nucleic
P–A · 649 Å² buried · 22 hydrogen bonds · protein-nucleic
P–T · 549 Å² buried · 47 hydrogen bonds · nucleic-nucleic

Compared structures

6X6Z · Rev1 Ternary Complex with dCTP and Ca2+ · 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 6X6Z · PDBe 6X6Z · UniProt P12689

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