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
- 6DBO
- Type
- protein + DNA
- Length
- 1,914 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 0.84
Structure
electron microscopy · 4 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 | 542 | 47% helix, 12% strand | P0AEX9, O13033 |
| B, D | Recombination activating gene 2 | protein | 351 | 1% helix, 45% strand | Q1RLW7 |
| E, G | Forward strand of substrate rss DNA | dna | 32 | — | — |
| F, H | Reverse strand of substrate rss DNA | dna | 32 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, E, C, G
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.84 | 0.89 | 54 | empty |
| 2 | 691 | 0.84 | 0.88 | 61 | empty |
| 3 | 528 | 0.80 | 0.87 | 65 | empty |
| 4 | 302 | 0.79 | 0.90 | 41 | empty |
| 5 | 859 | 0.77 | 0.81 | 56 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1947 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1936 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1394 Ų buried · 137 hydrogen bonds · nucleic-nucleic
- G–H · 1392 Ų buried · 131 hydrogen bonds · nucleic-nucleic
- A–C · 1238 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DBO · 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 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 6DBO · PDBe 6DBO · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7
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