Research workbench
Structure of the 10S (+)-trans-bp-dg modified REV1 ternary complex
Analyse Structure of the 10S (+)-trans-bp-dg modified REV1 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WM1
- Type
- protein + DNA
- Length
- 461 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
- 5 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3') | dna | 12 | — | — |
| T | DNA (5'- D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3') | dna | 16 | — | — |
| A | DNA repair protein REV1 (EC 2.7.7.-) | protein | 433 | 45% helix, 21% strand | P12689 |
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 · 8 copies · chains T, A
- GOL · Glycerol · additive · 5 copies · chains A, T
- PEG · Di(hydroxyethyl)ether · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.84 | 0.85 | 78 | empty |
| 2 | 1198 | 0.75 | 0.78 | 80 | MG, DCP, GOL |
| 3 | 180 | 0.57 | 0.81 | 25 | GOL, EDO |
| 4 | 97 | 0.36 | 0.74 | 22 | GOL, EDO |
| 5 | 77 | 0.33 | 0.74 | 16 | EDO |
Interfaces
3 interfaces between chains.
- T–A · 1375 Ų buried · 33 hydrogen bonds · protein-nucleic
- P–A · 689 Ų buried · 15 hydrogen bonds · protein-nucleic
- P–T · 549 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 5WM1 · Structure of the 10S (+)-trans-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 1.00
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 5WM1 · PDBe 5WM1 · UniProt P12689
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