Research workbench
Cryo-EM structure of mouse RAG1/2 prc complex (DNA0)
Analyse Cryo-EM structure of mouse RAG1/2 prc complex (DNA0) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OEM
- Type
- protein + DNA
- Length
- 2,206 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V(D)J recombination-activating protein 1; V(D)J recombination-activating protein 2; DNA…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784, P09429
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 9 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 606 | 49% helix, 11% strand | P15919 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 611 | 48% helix, 10% strand | P15919 |
| B, D | V(D)J recombination-activating protein 2 | protein | 346 | 1% helix, 45% strand | P21784 |
| G | DNA (57-mer) | dna | 57 | — | — |
| I | DNA (46-mer) | dna | 46 | — | — |
| F | DNA (46-mer) | dna | 46 | — | — |
| J | DNA (57-mer) | dna | 57 | — | — |
| N | High mobility group protein B1 | protein | 36 | 81% helix, 0% strand | P09429 |
| H | High mobility group protein B1 | protein | 55 | 84% helix, 0% strand | P09429 |
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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.84 | 0.86 | 78 | empty |
| 2 | 1104 | 0.84 | 0.86 | 99 | MG |
| 3 | 787 | 0.82 | 0.85 | 55 | empty |
| 4 | 829 | 0.81 | 0.84 | 66 | empty |
| 5 | 469 | 0.78 | 0.86 | 54 | empty |
Interfaces
21 interfaces between chains.
- A–C · 3343 Ų buried · 22 hydrogen bonds · protein-protein
- G–J · 2598 Ų buried · 173 hydrogen bonds · nucleic-nucleic
- C–D · 2072 Ų buried · 36 hydrogen bonds · protein-protein
- I–F · 2069 Ų buried · 135 hydrogen bonds · nucleic-nucleic
- A–B · 2030 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6OEM · Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) · the same entry in another collection · chain H against H, TM-score 1.00
- P21784 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 2 (P21784) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P15919 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (P15919) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 P15919
- Every structure of UniProt P21784
- Every structure of UniProt P09429
- Elsewhere: RCSB PDB 6OEM · PDBe 6OEM · UniProt P15919 · UniProt P21784 · UniProt P09429
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