MolNFT v1 · #159110 · protein + DNA
Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-nfc complex (DNA1)
6OEQ · V(D)J recombination-activating protein 1: “Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-nfc complex (DNA1)”. Electron microscopy, 2 ligands (ZN, CA), 20 pockets (best druggability 0.83). MolNFT v1 #159110 on GenesisL1: 3D…
- PDB
- 6OEQ
- Type
- protein + DNA
- Length
- 2,116 residues
- Chains
- 8
- 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
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 37% helix, 18% 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 | 46% helix, 11% strand | P15919 |
| B, D | V(D)J recombination-activating protein 2 | protein | 346 | 2% helix, 45% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 612 | 46% helix, 10% strand | P15919 |
| G | DNA (57-mer) | dna | 57 | — | — |
| J | DNA (57-mer) | dna | 57 | — | — |
| F | DNA (46-mer) | dna | 46 | — | — |
| I | DNA (46-mer) | dna | 46 | — | — |
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 | 801 | 0.83 | 0.86 | 73 | empty |
| 2 | 798 | 0.82 | 0.85 | 59 | empty |
| 3 | 830 | 0.82 | 0.84 | 74 | empty |
| 4 | 606 | 0.79 | 0.85 | 61 | empty |
| 5 | 425 | 0.78 | 0.87 | 61 | empty |
Interfaces
17 interfaces between chains.
- A–C · 3102 Ų buried · 13 hydrogen bonds · protein-protein
- G–J · 2746 Ų buried · 207 hydrogen bonds · nucleic-nucleic
- F–I · 2123 Ų buried · 165 hydrogen bonds · nucleic-nucleic
- A–B · 2007 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1976 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6OEQ · Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-NFC complex (DNA1) · the same entry in another collection · chain I against I, 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 0.96
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
- Elsewhere: RCSB PDB 6OEQ · PDBe 6OEQ · UniProt P15919 · UniProt P21784
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