Research workbench
Cryo-EM structure of recbcd-DNA complex with docked recbnuc and stabilized recd
Analyse Cryo-EM structure of recbcd-DNA complex with docked recbnuc and stabilized recd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MR3
- Type
- protein + DNA
- Length
- 2,894 residues
- Chains
- 5
- 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 0.86
Structure
electron microscopy · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Recbcd enzyme subunit recb (EC 3.1.11.5) | protein | 1128 | 48% helix, 11% strand | P08394 |
| C | Recbcd enzyme subunit recc (EC 3.1.11.5) | protein | 1121 | 48% helix, 11% strand | P07648 |
| D | Recbcd enzyme subunit recd (EC 3.1.11.5) | protein | 605 | 44% helix, 14% strand | P04993 |
| X | DNA (60-mer) | dna | 24 | — | — |
| A | DNA (60-mer) | dna | 16 | — | — |
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 | 1121 | 0.86 | 0.87 | 140 | empty |
| 2 | 1140 | 0.79 | 0.81 | 109 | empty |
| 3 | 1000 | 0.78 | 0.81 | 76 | empty |
| 4 | 1082 | 0.76 | 0.79 | 120 | empty |
| 5 | 476 | 0.75 | 0.84 | 51 | empty |
Interfaces
9 interfaces between chains.
- B–C · 7451 Ų buried · 71 hydrogen bonds · protein-protein
- C–D · 1351 Ų buried · 16 hydrogen bonds · protein-protein
- D–X · 963 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–A · 951 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–X · 770 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 7MR3 · Cryo-EM structure of RecBCD-DNA complex with docked RecBNuc and stabilized RecD · the same entry in another collection · chain A against A, 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 0.96
- 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
- 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 0.82
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 7MR3 · PDBe 7MR3 · UniProt P08394 · UniProt P07648 · UniProt P04993
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