Research workbench
Cryo-EM structure of RECBCD+DNA complex revealing activated nuclease domain
Analyse Cryo-EM structure of RECBCD+DNA complex revealing activated nuclease domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LD2
- Type
- protein + DNA
- Length
- 2,928 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recbcd enzyme subunit RECB,RECBCD enzyme subunit recb, recbcd enzyme subunit recb; Recbcd…
- EC
- 3.1.11.5
- UniProt
- P08394, P07648, P04993
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Recbcd enzyme subunit RECB,RECBCD enzyme subunit recb, recbcd enzyme subunit recb (EC 3.1.11.5) | protein | 1151 | 48% helix, 13% strand | P08394 |
| C | Recbcd enzyme subunit recc (EC 3.1.11.5) | protein | 1121 | 47% helix, 12% strand | P07648 |
| D | Recbcd enzyme subunit recd (EC 3.1.11.5) | protein | 605 | 44% helix, 15% strand | P04993 |
| X | Fork-hairpin DNA (70-mer) | dna | 51 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains B
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 | 756 | 0.82 | 0.85 | 87 | empty |
| 2 | 881 | 0.80 | 0.83 | 94 | empty |
| 3 | 586 | 0.77 | 0.84 | 68 | empty |
| 4 | 521 | 0.75 | 0.83 | 55 | empty |
| 5 | 504 | 0.73 | 0.82 | 65 | ANP, MG |
Interfaces
6 interfaces between chains.
- B–C · 7345 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 1386 Ų buried · 10 hydrogen bonds · protein-protein
- B–X · 1247 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–X · 958 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–X · 783 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5LD2 · Cryo-EM structure of RecBCD+DNA complex revealing activated nuclease domain · 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 0.96
- 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 5LD2 · PDBe 5LD2 · UniProt P08394 · UniProt P07648 · UniProt P04993
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