MolNFT v1 · #163976 · protein + DNA
Cryo-EM structure of the recbcd chi partially-recognised complex
6SJE · Recbcd enzyme subunit recb: “Cryo-EM structure of the recbcd chi partially-recognised complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #163976 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6SJE
- Type
- protein + DNA
- Length
- 2,915 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; DNA…
- EC
- 3.1.11.5
- UniProt
- P08394, P07648, P04993
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 46% helix, 12% 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 | 45% helix, 10% strand | P07648 |
| D | Recbcd enzyme subunit recd (EC 3.1.11.5) | protein | 597 | 43% helix, 14% strand | P04993 |
| X | DNA fork substrate | dna | 68 | — | — |
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 | 1131 | 0.85 | 0.87 | 107 | empty |
| 2 | 1041 | 0.82 | 0.83 | 105 | empty |
| 3 | 875 | 0.81 | 0.83 | 89 | empty |
| 4 | 736 | 0.79 | 0.83 | 97 | empty |
| 5 | 712 | 0.74 | 0.80 | 79 | empty |
Interfaces
6 interfaces between chains.
- B–C · 7495 Ų buried · 73 hydrogen bonds · protein-protein
- C–X · 2427 Ų buried · 48 hydrogen bonds · protein-nucleic
- B–X · 2277 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–D · 1504 Ų buried · 12 hydrogen bonds · protein-protein
- D–X · 1108 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6SJE · Cryo-EM structure of the RecBCD Chi partially-recognised complex · the same entry in another collection · chain B against B, TM-score 1.00
- 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
- 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 0.95
- 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 0.81
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 6SJE · PDBe 6SJE · UniProt P08394 · UniProt P07648 · UniProt P04993
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