MolNFT v1 · #159111 · protein + DNA
Cryo-EM structure of mouse RAG1/2 nfc complex (DNA2)
6OER · V(D)J recombination-activating protein 1: “Cryo-EM structure of mouse RAG1/2 nfc complex (DNA2)”. Electron microscopy, 2 ligands (CA, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #159111 on GenesisL1: 3D structure, binding…
- PDB
- 6OER
- Type
- protein + DNA
- Length
- 2,158 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, Q08IE6
- Ligands
- CA, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 8 distinct chains · 38% 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 | 608 | 49% helix, 11% strand | P15919 |
| B, D | V(D)J recombination-activating protein 2 | protein | 346 | 1% helix, 45% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 616 | 47% 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 | — | — |
| H | High mobility group protein B1 | protein | 36 | 58% helix, 0% strand | Q08IE6 |
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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.87 | 0.88 | 73 | empty |
| 2 | 701 | 0.83 | 0.87 | 60 | empty |
| 3 | 730 | 0.82 | 0.85 | 61 | empty |
| 4 | 300 | 0.78 | 0.90 | 44 | empty |
| 5 | 260 | 0.77 | 0.90 | 43 | empty |
Interfaces
20 interfaces between chains.
- A–C · 3374 Ų buried · 17 hydrogen bonds · protein-protein
- G–J · 2646 Ų buried · 168 hydrogen bonds · nucleic-nucleic
- F–I · 2146 Ų buried · 140 hydrogen bonds · nucleic-nucleic
- A–B · 2068 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1986 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6OER · Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2) · 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 0.99
- 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 0.97
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 P15919
- Every structure of UniProt P21784
- Every structure of UniProt Q08IE6
- Elsewhere: RCSB PDB 6OER · PDBe 6OER · UniProt P15919 · UniProt P21784 · UniProt Q08IE6
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