Research workbench
Cryo-EM structure of RAG in complex with 12-RSS substrate DNA
Analyse Cryo-EM structure of RAG in complex with 12-RSS substrate DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DBW
- Type
- protein + DNA
- Length
- 2,031 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.7
- Source
- Danio rerio; Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- Recombination activating gene 1 - MBP chimera; Recombination activating gene 2; Forward…
- EC
- 2.3.2.27
- UniProt
- P0AEX9, O13033, Q1RLW7
- Ligands
- CA, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 4.7 · 5 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Recombination activating gene 1 - MBP chimera (EC 2.3.2.27) | protein | 614 | 50% helix, 11% strand | P0AEX9, O13033 |
| B, D | Recombination activating gene 2 | protein | 351 | 1% helix, 42% strand | Q1RLW7 |
| C | Recombination activating gene 1 - MBP chimera (EC 2.3.2.27) | protein | 615 | 50% helix, 10% strand | P0AEX9, O13033 |
| E | Forward strand of 12-RSS substrate DNA | dna | 50 | — | — |
| F | Reverse strand of 12-RSS substrate DNA | dna | 50 | — | — |
Ligands and binding sites
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 | 902 | 0.86 | 0.88 | 102 | empty |
| 2 | 835 | 0.83 | 0.86 | 80 | empty |
| 3 | 1031 | 0.83 | 0.84 | 92 | empty |
| 4 | 588 | 0.82 | 0.87 | 65 | empty |
| 5 | 126 | 0.77 | 0.95 | 41 | empty |
Interfaces
10 interfaces between chains.
- A–C · 3321 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2213 Ų buried · 211 hydrogen bonds · nucleic-nucleic
- C–D · 1912 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1902 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 1137 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 6DBW · Cryo-EM structure of rag in complex with 12-rss substrate DNA · the same entry in another collection · chain F against F, TM-score 1.00
- O13033 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (O13033) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P0AEX9
- Every structure of UniProt O13033
- Every structure of UniProt Q1RLW7
- Elsewhere: RCSB PDB 6DBW · PDBe 6DBW · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7
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