MolNFT v1 · #163978 · protein + DNA
Cryo-EM structure of the recbcd no chi negative control complex
6SJG · Recbcd enzyme subunit recb: “Cryo-EM structure of the recbcd no chi negative control complex”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #163978 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SJG
- Type
- protein + DNA
- Length
- 2,901 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recbcd enzyme subunit recb; Recbcd enzyme subunit recc; Recbcd enzyme subunit recd…
- EC
- 3.1.11.5
- UniProt
- P08394, P07648, P04993
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Recbcd enzyme subunit recb (EC 3.1.11.5) | protein | 1129 | 47% helix, 13% strand | P08394 |
| C | Recbcd enzyme subunit recc (EC 3.1.11.5) | protein | 1121 | 47% helix, 11% strand | P07648 |
| D | Recbcd enzyme subunit recd (EC 3.1.11.5) | protein | 597 | 42% helix, 14% strand | P04993 |
| X | Forked DNA substrate | dna | 54 | — | — |
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 | 852 | 0.83 | 0.85 | 108 | empty |
| 2 | 542 | 0.81 | 0.87 | 61 | empty |
| 3 | 692 | 0.79 | 0.84 | 60 | empty |
| 4 | 408 | 0.77 | 0.86 | 54 | empty |
| 5 | 894 | 0.76 | 0.79 | 74 | empty |
Interfaces
6 interfaces between chains.
- B–C · 7753 Ų buried · 76 hydrogen bonds · protein-protein
- B–X · 1730 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–D · 1468 Ų buried · 11 hydrogen bonds · protein-protein
- D–X · 1093 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–X · 939 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6SJG · Cryo-EM structure of the RecBCD no Chi negative control complex · the same entry in another collection · chain B against B, 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 0.96
- 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 0.95
- 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 0.83
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 6SJG · PDBe 6SJG · UniProt P08394 · UniProt P07648 · UniProt P04993
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