MolNFT v1 · #146235 · protein + DNA
Cryo-EM structure of rag in complex with 12-rss and 23-rss nicked DNA intermediates
6DBJ · Recombination activating gene 1 - mbp chimera: “Cryo-EM structure of rag in complex with 12-rss and 23-rss nicked DNA intermediates”. Electron microscopy, 2 ligands (CA, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #146235 on…
- PDB
- 6DBJ
- Type
- protein + DNA
- Length
- 1,932 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 · 5 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Recombination activating gene 1 - mbp chimera (EC 2.3.2.27) | protein | 552 | 46% helix, 13% strand | P0AEX9, O13033 |
| B, D | Recombination activating gene 2 | protein | 352 | 1% helix, 45% strand | Q1RLW7 |
| E, H | Forward stand of rss signal end | dna | 15 | — | — |
| F, G | Reverse stand of rss | dna | 31 | — | — |
| I, J | Forward strand of coding flank | dna | 16 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, G, I, C, F, J
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.87 | 0.88 | 94 | empty |
| 2 | 920 | 0.86 | 0.88 | 107 | empty |
| 3 | 894 | 0.86 | 0.88 | 91 | empty |
| 4 | 420 | 0.80 | 0.88 | 58 | empty |
| 5 | 244 | 0.78 | 0.92 | 37 | empty |
Interfaces
23 interfaces between chains.
- A–C · 1979 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1902 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1893 Ų buried · 33 hydrogen bonds · protein-protein
- A–G · 955 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–F · 940 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 6DBJ · 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 A against A, TM-score 0.99
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 6DBJ · PDBe 6DBJ · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7
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