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MolNFT v1 · #138535 · protein + DNA

Structure of the 10R (+)-cis-bp-dg modified REV1 ternary complex

5WM8 · DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3'): “Structure of the 10R (+)-cis-bp-dg modified REV1 ternary complex”. X-ray diffraction, 3 ligands (BAP, DCP, MG), 4 pockets (best druggability 0.83). MolNFT v1 #138535 on…

PDB
5WM8
Type
protein + DNA
Length
460 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*(DDG))-3'); DNA (5'…
EC
2.7.7.-
UniProt
P12689
Ligands
BAP, DCP, MG
Pockets
4 · best druggability 0.83

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
PDNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3')dna12——
TDNA (5'- D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')dna16——
ADNA repair protein REV1 (EC 2.7.7.-)protein43244% helix, 21% strandP12689

Ligands and binding sites

  • BAP · 1,2,3-trihydroxy-1,2,3,4-tetrahydrobenzo[a]pyrene · ligand · chains T, A
  • DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, A
  • MG · Magnesium ion · metal · 4 copies · chains P, A
  • EDO · 1,2-ethanediol · additive · 9 copies · chains T, A, P
  • GOL · Glycerol · additive · 3 copies · chains A, P, T
  • PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110570.830.8472EDO
210320.790.8177MG, DCP, GOL, EDO
31930.560.8025GOL
4730.360.7615EDO

Interfaces

3 interfaces between chains.

  • T–A · 1400 Ų buried · 36 hydrogen bonds · protein-nucleic
  • P–A · 668 Ų buried · 18 hydrogen bonds · protein-nucleic
  • P–T · 542 Ų buried · 52 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 5WM8 · Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex · 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

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