Research workbench
Cryo-EM structure of rag in complex with 12-rss and 23-rss nicked DNA intermediates
Analyse Cryo-EM structure of rag in complex with 12-rss and 23-rss nicked DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DBI
- Type
- protein + DNA
- Length
- 2,168 residues
- Chains
- 10
- 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 · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Recombination activating gene 1 - mbp chimera (EC 2.3.2.27) | protein | 622 | 46% helix, 10% strand | P0AEX9, O13033 |
| D, B | Recombination activating gene 2 | protein | 351 | 1% helix, 44% strand | Q1RLW7 |
| E | Forward strand of 12-rss signal end | dna | 34 | — | — |
| F | Reverse strand of 12-rss | dna | 50 | — | — |
| G | Reverse strand of 23-rss | dna | 61 | — | — |
| H | Forward strand of 23-rss signal end | dna | 45 | — | — |
| I, J | Forward strand of coding flank | dna | 16 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C, G, J, A, F, I
- ZN · Zinc ion · metal · 2 copies · chains C, A
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 | 1049 | 0.87 | 0.88 | 102 | empty |
| 2 | 911 | 0.86 | 0.88 | 85 | empty |
| 3 | 463 | 0.83 | 0.90 | 53 | empty |
| 4 | 336 | 0.78 | 0.89 | 52 | empty |
| 5 | 242 | 0.78 | 0.91 | 41 | empty |
Interfaces
23 interfaces between chains.
- C–A · 3875 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 1986 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- A–B · 1916 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1869 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1493 Ų buried · 109 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DBI · Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates · the same entry in another collection · chain J against J, 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 0.98
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 6DBI · PDBe 6DBI · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.