Research workbench
Structure of human REV1-DNA-dntp ternary complex
Analyse Structure of human REV1-DNA-dntp ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GQC
- Type
- protein + DNA
- Length
- 1,843 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein REV1; 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'…
- EC
- 2.7.7.-
- UniProt
- Q9UBZ9
- Ligands
- DCP, MG
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein REV1 (EC 2.7.7.-) | protein | 435 | 45% helix, 20% strand | Q9UBZ9 |
| B | DNA repair protein REV1 (EC 2.7.7.-) | protein | 440 | 44% helix, 19% strand | Q9UBZ9 |
| C | DNA repair protein REV1 (EC 2.7.7.-) | protein | 423 | 44% helix, 20% strand | Q9UBZ9 |
| D | DNA repair protein REV1 (EC 2.7.7.-) | protein | 433 | 44% helix, 19% strand | Q9UBZ9 |
| E, G, I, K | 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3' | dna | 12 | — | — |
| F, H, J, L | 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3' | dna | 16 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 4 copies · chains A, E, B, G, C, I, D, K
- MG · Magnesium ion · metal · 13 copies · chains A, E, F, B, G, C, I, D, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.79 | 0.81 | 80 | DCP, MG |
| 2 | 523 | 0.79 | 0.86 | 54 | DCP, MG |
| 3 | 523 | 0.79 | 0.86 | 53 | empty |
| 4 | 782 | 0.78 | 0.82 | 63 | empty |
| 5 | 907 | 0.77 | 0.80 | 56 | empty |
Interfaces
18 interfaces between chains.
- B–H · 1441 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–F · 1427 Ų buried · 40 hydrogen bonds · protein-nucleic
- D–L · 1417 Ų buried · 38 hydrogen bonds · protein-nucleic
- C–J · 1416 Ų buried · 37 hydrogen bonds · protein-nucleic
- G–H · 527 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3GQC · Structure of human Rev1-DNA-dNTP ternary complex · the same entry in another collection · chain L against L, 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 Q9UBZ9
- Elsewhere: RCSB PDB 3GQC · PDBe 3GQC · UniProt Q9UBZ9
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