MolNFT v1 · #169816 · protein + DNA
Structure of RAG1 (R848M/E649V)-RAG2-DNA target capture complex
6XNZ · V(D)J recombination-activating protein 1: “Structure of RAG1 (R848M/E649V)-RAG2-DNA target capture complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #169816 on GenesisL1: 3D structure…
- PDB
- 6XNZ
- Type
- protein + DNA
- Length
- 1,901 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…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 29% 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 | 550 | 45% helix, 8% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 343 | 1% helix, 32% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 549 | 46% helix, 8% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 343 | 3% helix, 30% strand | P21784 |
| I | Target DNA top strand (37-mer) | dna | 31 | — | — |
| J | Target DNA bottom strand (37-mer) | dna | 31 | — | — |
| x | 12RSS integration strand (34-mer) | dna | 15 | — | — |
| M | 12RSS non-integration strand (34-mer) | dna | 15 | — | — |
| y | 23RSS integration strand (45-mer) | dna | 12 | — | — |
| L | 23RSS non-integration strand (45-mer) | dna | 12 | — | — |
Ligands and binding sites
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.81 | 0.91 | 49 | empty |
| 2 | 271 | 0.80 | 0.92 | 46 | empty |
| 3 | 281 | 0.80 | 0.92 | 33 | empty |
| 4 | 225 | 0.80 | 0.93 | 35 | empty |
| 5 | 654 | 0.80 | 0.84 | 60 | empty |
Interfaces
26 interfaces between chains.
- A–B · 2140 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 2097 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2080 Ų buried · 46 hydrogen bonds · protein-protein
- I–J · 1620 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- C–I · 921 Ų buried · 28 hydrogen bonds · protein-nucleic
Compared structures
- 6XNZ · Structure of RAG1 (R848M/E649V)-RAG2-DNA Target Capture Complex · the same entry in another collection · chain L against L, TM-score 1.00
- 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 0.98
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 6XNZ · PDBe 6XNZ · UniProt P15919 · UniProt P21784
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