Research workbench
Structure of RAG1 (R848M/E649V)-RAG2-DNA strand transfer complex (dynamic-form)
Analyse Structure of RAG1 (R848M/E649V)-RAG2-DNA strand transfer complex (dynamic-form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XNX
- Type
- protein + DNA
- Length
- 1,898 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 0.86
Structure
electron microscopy · 9 distinct chains · 30% helix, 25% 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 | 549 | 47% helix, 12% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 342 | 3% helix, 40% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 548 | 48% helix, 13% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 343 | 3% helix, 48% strand | P21784 |
| x | 12RSS integration strand DNA (55-mer) | dna | 32 | — | — |
| y | 23RSS integration strand DNA (66-mer) | dna | 28 | — | — |
| I, J | Flanking DNA top strand DNA | dna | 14 | — | — |
| L | 23RSS signal top strand DNA (45-mer) | dna | 12 | — | — |
| M | 12RSS signal top strand DNA (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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.86 | 0.87 | 112 | empty |
| 2 | 1028 | 0.84 | 0.85 | 120 | empty |
| 3 | 523 | 0.83 | 0.90 | 79 | empty |
| 4 | 470 | 0.82 | 0.89 | 51 | empty |
| 5 | 450 | 0.79 | 0.87 | 51 | empty |
Interfaces
26 interfaces between chains.
- C–D · 2120 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 2076 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 1895 Ų buried · 27 hydrogen bonds · protein-protein
- A–x · 907 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–y · 859 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 6XNX · Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-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 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 6XNX · PDBe 6XNX · UniProt P15919 · UniProt P21784
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