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
- 6DBX
- Type
- protein + DNA
- Length
- 2,033 residues
- Chains
- 6
- 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 0.83
Structure
electron microscopy · 6 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Recombination activating gene 1 - mbp chimera (EC 2.3.2.27) | protein | 615 | 49% helix, 11% strand | P0AEX9, O13033 |
| B | Recombination activating gene 2 | protein | 351 | 2% helix, 37% strand | Q1RLW7 |
| C | Recombination activating gene 1 - mbp chimera (EC 2.3.2.27) | protein | 615 | 48% helix, 10% strand | P0AEX9, O13033 |
| D | Recombination activating gene 2 | protein | 352 | 1% helix, 41% strand | Q1RLW7 |
| 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.83 | 0.86 | 96 | empty |
| 2 | 951 | 0.83 | 0.84 | 87 | empty |
| 3 | 1137 | 0.82 | 0.83 | 96 | empty |
| 4 | 85 | 0.69 | 0.93 | 22 | empty |
| 5 | 193 | 0.67 | 0.86 | 30 | empty |
Interfaces
10 interfaces between chains.
- A–C · 3379 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2235 Ų buried · 186 hydrogen bonds · nucleic-nucleic
- C–D · 1921 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1789 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 895 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6DBX · 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 6DBX · PDBe 6DBX · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7
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