Research workbench
Cryo-EM structure of mouse RAG1/2 nfc complex (DNA1)
Analyse Cryo-EM structure of mouse RAG1/2 nfc complex (DNA1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OEO
- Type
- protein + DNA
- Length
- 2,176 residues
- Chains
- 9
- 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
- CA, ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 distinct chains · 38% 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 | 608 | 46% helix, 11% strand | P15919 |
| B, D | V(D)J recombination-activating protein 2 | protein | 346 | 2% helix, 44% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 616 | 46% helix, 10% strand | P15919 |
| F | DNA (46-mer) | dna | 46 | — | — |
| I | DNA (46-mer) | dna | 46 | — | — |
| G | DNA (57-mer) | dna | 57 | — | — |
| J | DNA (57-mer) | dna | 57 | — | — |
| N | High mobility group protein B1 | protein | 54 | 76% helix, 0% strand | P09429 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, I, C, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.81 | 0.85 | 57 | empty |
| 2 | 788 | 0.81 | 0.84 | 64 | empty |
| 3 | 339 | 0.79 | 0.90 | 34 | empty |
| 4 | 228 | 0.77 | 0.92 | 31 | empty |
| 5 | 364 | 0.77 | 0.88 | 51 | empty |
Interfaces
19 interfaces between chains.
- A–C · 3292 Ų buried · 18 hydrogen bonds · protein-protein
- G–J · 2715 Ų buried · 184 hydrogen bonds · nucleic-nucleic
- F–I · 2237 Ų buried · 163 hydrogen bonds · nucleic-nucleic
- A–B · 2011 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1927 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6OEO · Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) · the same entry in another collection · chain N against N, 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 0.99
- 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 0.95
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 6OEO · PDBe 6OEO · UniProt P15919 · UniProt P21784 · UniProt P09429
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