Research workbench
Cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas
Analyse Cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DBV
- Type
- protein + DNA
- Length
- 2,161 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 0.87
Structure
electron microscopy · 7 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Recombination activating gene 1 - mbp chimera (EC 2.3.2.27) | protein | 616 | 48% helix, 10% strand | P0AEX9, O13033 |
| B, D | Recombination activating gene 2 | protein | 351 | 3% helix, 40% strand | Q1RLW7 |
| C | Recombination activating gene 1 - mbp chimera (EC 2.3.2.27) | protein | 621 | 48% helix, 9% strand | P0AEX9, O13033 |
| E | Forward strand of 12-rss substrate DNA | dna | 50 | — | — |
| F | Reverse strand of 12-rss substrate DNA | dna | 50 | — | — |
| G | Forward strand of 23-rss substrate DNA | dna | 61 | — | — |
| H | Reverse strand of 23-rss substrate DNA | dna | 61 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, E, C, H
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.87 | 0.89 | 74 | empty |
| 2 | 776 | 0.86 | 0.89 | 81 | empty |
| 3 | 906 | 0.85 | 0.86 | 84 | empty |
| 4 | 297 | 0.78 | 0.90 | 44 | empty |
| 5 | 1178 | 0.75 | 0.78 | 92 | CA |
Interfaces
17 interfaces between chains.
- A–C · 3417 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2790 Ų buried · 227 hydrogen bonds · nucleic-nucleic
- E–F · 2186 Ų buried · 185 hydrogen bonds · nucleic-nucleic
- A–B · 1846 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1844 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6DBV · Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs · the same entry in another collection · chain H against H, 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 0.92
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 6DBV · PDBe 6DBV · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7
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