MolNFT v1 · #68805 · protein + DNA
Crystal structure of the complete initiation complex of recbcd
3K70 · Exodeoxyribonuclease V beta chain: “Crystal structure of the complete initiation complex of recbcd”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.87). MolNFT v1 #68805 on GenesisL1: 3D structure, binding sites…
- PDB
- 3K70
- Type
- protein + DNA
- Length
- 5,738 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 0.87
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | Exodeoxyribonuclease V beta chain (EC 3.1.11.5) | protein | 1155 | 46% helix, 11% strand | P08394 |
| C, F | Exodeoxyribonuclease V gamma chain (EC 3.1.11.5) | protein | 1121 | 45% helix, 10% strand | P07648 |
| D, G | Exodeoxyribonuclease V alpha chain (EC 3.1.11.5) | protein | 547 | 40% helix, 13% strand | P04993 |
| X, Y | DNA (46-mer) | dna | 46 | — | — |
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 | 919 | 0.87 | 0.89 | 118 | empty |
| 2 | 1040 | 0.85 | 0.87 | 112 | empty |
| 3 | 541 | 0.84 | 0.90 | 83 | CA |
| 4 | 934 | 0.83 | 0.85 | 98 | empty |
| 5 | 455 | 0.80 | 0.88 | 59 | CA |
Interfaces
13 interfaces between chains.
- B–C · 8220 Ų buried · 102 hydrogen bonds · protein-protein
- E–F · 8209 Ų buried · 103 hydrogen bonds · protein-protein
- E–Y · 1615 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–X · 1589 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–G · 1260 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (nucleotide modification).
Compared structures
- 3K70 · Crystal structure of the complete initiation complex of RecBCD · the same entry in another collection · chain Y against Y, TM-score 1.00
- P07648 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recc (P07648) · a predicted model of the same protein · chain C 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 0.92
- 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 3K70 · PDBe 3K70 · UniProt P08394 · UniProt P07648 · UniProt P04993
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