MolNFT v1 · #169815 · protein + DNA
Structure of RAG1 (R848M/E649V)-RAG2-DNA strand transfer complex (paired-form)
6XNY · V(D)J recombination-activating protein 1: “Structure of RAG1 (R848M/E649V)-RAG2-DNA strand transfer complex (paired-form)”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #169815 on…
- PDB
- 6XNY
- Type
- protein + DNA
- Length
- 1,909 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; 12RSS…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 30% helix, 24% 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 | 47% helix, 11% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 344 | 3% helix, 41% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 548 | 46% helix, 13% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 345 | 3% helix, 45% strand | P21784 |
| x | 12RSS integration strand (55-mer) | dna | 35 | — | — |
| y | 23RSS integration strand (66-mer) | dna | 31 | — | — |
| I, J | Flanking DNA top strand (16-mer) | dna | 14 | — | — |
| L | 23RSS signal DNA top strand (45-mer) | dna | 12 | — | — |
| M | 12RSS signal DNA top strand (34-mer) | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, y, I, C, x, 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 | 637 | 0.88 | 0.93 | 104 | empty |
| 2 | 364 | 0.85 | 0.95 | 72 | empty |
| 3 | 471 | 0.80 | 0.87 | 52 | empty |
| 4 | 425 | 0.79 | 0.87 | 51 | empty |
| 5 | 231 | 0.79 | 0.92 | 41 | empty |
Interfaces
28 interfaces between chains.
- C–D · 2191 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2055 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 1978 Ų buried · 25 hydrogen bonds · protein-protein
- A–x · 921 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–y · 918 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 6XNY · Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form) · the same entry in another collection · chain M against M, 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 C 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 6XNY · PDBe 6XNY · UniProt P15919 · UniProt P21784
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