MolNFT v1 · #25702 · protein + DNA
RECBCD:DNA complex
1W36 · Exodeoxyribonuclease V beta chain: “RECBCD:DNA complex”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.81). MolNFT v1 #25702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1W36
- Type
- protein + DNA
- Length
- 5,666 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease V beta chain; Exodeoxyribonuclease V gamma chain…
- EC
- 3.1.11.5
- UniProt
- P08394, P07648, P04993
- Ligands
- CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | Exodeoxyribonuclease V beta chain (EC 3.1.11.5) | protein | 1158 | 47% helix, 12% strand | P08394 |
| C | Exodeoxyribonuclease V gamma chain (EC 3.1.11.5) | protein | 1121 | 47% helix, 11% strand | P07648 |
| D, G | Exodeoxyribonuclease V alpha chain (EC 3.1.11.5) | protein | 538 | 40% helix, 11% strand | P04993 |
| F | Exodeoxyribonuclease V gamma chain (EC 3.1.11.5) | protein | 1077 | 48% helix, 11% strand | P07648 |
| Y, Z | DNA hairpin | dna | 38 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.81 | 0.83 | 120 | empty |
| 2 | 1063 | 0.81 | 0.82 | 124 | empty |
| 3 | 937 | 0.80 | 0.83 | 106 | empty |
| 4 | 543 | 0.80 | 0.87 | 84 | empty |
| 5 | 676 | 0.80 | 0.85 | 64 | empty |
Interfaces
10 interfaces between chains.
- B–C · 8277 Ų buried · 118 hydrogen bonds · protein-protein
- E–F · 8265 Ų buried · 121 hydrogen bonds · protein-protein
- B–Y · 1343 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–Z · 1306 Ų buried · 17 hydrogen bonds · protein-nucleic
- F–G · 1241 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- P07648 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recc (P07648) · a predicted model of the same protein · chain F against A, TM-score 0.97
- P04993 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recd (P04993) · a predicted model of the same protein · chain D against A, TM-score 0.91
- P08394 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recb (P08394) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 P08394
- Every structure of UniProt P07648
- Every structure of UniProt P04993
- Elsewhere: RCSB PDB 1W36 · PDBe 1W36 · UniProt P08394 · UniProt P07648 · UniProt P04993
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