MolNFT v1 · #166790 · protein + DNA
Cryo-EM structure of mouse wt RAG1/2 nfc complex (DNA0)
6V0V · V(D)J recombination-activating protein 1: “Cryo-EM structure of mouse wt RAG1/2 nfc complex (DNA0)”. Electron microscopy, 2 ligands (CA, ZN), 15 pockets (best druggability 0.86). MolNFT v1 #166790 on GenesisL1: 3D structure, binding…
- PDB
- 6V0V
- Type
- protein + DNA
- Length
- 947 residues
- Chains
- 4
- 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
- CA, ZN
- Pockets
- 15 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 28% helix, 26% 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 | 541 | 45% helix, 13% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 346 | 1% helix, 48% strand | P21784 |
| F | DNA (30-mer) | dna | 30 | — | — |
| I | DNA (30-mer) | dna | 30 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.86 | 0.88 | 127 | empty |
| 2 | 615 | 0.73 | 0.80 | 44 | empty |
| 3 | 76 | 0.69 | 0.93 | 22 | empty |
| 4 | 60 | 0.57 | 0.89 | 24 | empty |
| 5 | 163 | 0.52 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1915 Ų buried · 30 hydrogen bonds · protein-protein
- F–I · 1430 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–I · 946 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–F · 451 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–F · 150 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6V0V · Cryo-EM structure of mouse WT RAG1/2 NFC complex (DNA0) · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.99
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 6V0V · PDBe 6V0V · UniProt P15919 · UniProt P21784
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