Research workbench
Catalytic core of REV1 in complex with DNA (modified template guanine) and incoming nucleotide
Analyse Catalytic core of REV1 in complex with DNA (modified template guanine) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BJY
- 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; DNA (5'-D(*DTP*DAP*DAP*(P)…
- EC
- 2.7.7.-
- UniProt
- P12689
- Ligands
- DCP, MG
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein REV1 (EC 2.7.7.-) | protein | 428 | 44% helix, 20% strand | P12689 |
| T | DNA (5'-D(*DTP*DAP*DAP*(P) P*DGP*DTP*DAP*DGP*DGP*DGP*DGP*DAP*DGP*DGP*DAP*DT)-3') | dna | 16 | — | — |
| P | DNA (5'- D(*DAP*DTP*DCP*DCP*DTP*DCP*DCP*DCP*DCP*DTP*DAP*(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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.86 | 0.87 | 77 | DCP, MG |
| 2 | 422 | 0.71 | 0.83 | 41 | empty |
| 3 | 177 | 0.54 | 0.80 | 28 | empty |
| 4 | 212 | 0.53 | 0.77 | 31 | empty |
| 5 | 72 | 0.35 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1469 Ų buried · 37 hydrogen bonds · protein-nucleic
- A–P · 620 Ų buried · 20 hydrogen bonds · protein-nucleic
- T–P · 524 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3BJY · Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming… · 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 3BJY · PDBe 3BJY · UniProt P12689
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