Research workbench
REV1 ternary complex with dgtp and CA2+
Analyse REV1 ternary complex with dgtp and CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T19
- 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
- DGT, CA
- Pockets
- 6 · 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(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3') | dna | 12 | — | — |
| 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
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains P, A
- CA · Calcium ion · metal · 2 copies · chains P, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.84 | 0.85 | 77 | CA, DGT |
| 2 | 472 | 0.71 | 0.81 | 39 | empty |
| 3 | 217 | 0.56 | 0.79 | 25 | empty |
| 4 | 99 | 0.50 | 0.82 | 18 | empty |
| 5 | 54 | 0.38 | 0.80 | 14 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1340 Ų buried · 34 hydrogen bonds · protein-nucleic
- P–A · 610 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 548 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
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 7T19 · PDBe 7T19 · UniProt P12689
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