Research workbench
REV1 MG2+-facilitated intermediate complex with reactant dctp and product dcmp
Analyse REV1 MG2+-facilitated intermediate complex with reactant dctp and product dcmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X71
- Type
- protein + DNA
- Length
- 467 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*GP*C*(MG))-3'); DNA (5'…
- EC
- 2.7.7.-
- UniProt
- P12689
- Ligands
- DCP, POP, MG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*C*(MG))-3') | dna | 13 | — | — |
| T | DNA (5'- D(*CP*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 | 438 | 43% helix, 20% strand | P12689 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, A
- POP · Pyrophosphate 2- · ligand · chains P, A
- MG · Magnesium ion · metal · 4 copies · chains P, A
- GOL · Glycerol · additive · 3 copies · chains P, T, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.82 | 0.84 | 70 | MG, POP |
| 2 | 615 | 0.73 | 0.81 | 46 | GOL |
| 3 | 208 | 0.59 | 0.81 | 27 | empty |
| 4 | 235 | 0.58 | 0.79 | 29 | GOL |
| 5 | 77 | 0.40 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1389 Ų buried · 37 hydrogen bonds · protein-nucleic
- P–A · 855 Ų buried · 29 hydrogen bonds · protein-nucleic
- P–T · 550 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6X71 · Rev1 Mg2+-facilitated Intermediate complex with reactant dCTP and product dCMP · the same entry in another collection · chain T against T, 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 6X71 · PDBe 6X71 · UniProt P12689
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