MolNFT v2 · #160221 · protein + DNA
Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)
6OES · V(D)J recombination-activating protein 1: “Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)”. Electron microscopy at 3.06, 2 ligands (CA, ZN), 20 pockets (best druggability 0.87). MolNFT v2 #160221 on GenesisL1: 3D…
- PDB
- 6OES
- Type
- protein + DNA
- Length
- 1,912 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.06
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- 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
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.06 · 9 distinct chains · 29% 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 | 548 | 45% helix, 13% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 344 | 2% helix, 45% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 547 | 46% helix, 12% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 345 | 2% helix, 46% strand | P21784 |
| F | DNA (35-mer) | dna | 35 | — | — |
| J, I | DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3') | dna | 15 | — | — |
| G | DNA (34-mer) | dna | 34 | — | — |
| L | DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3') | dna | 15 | — | — |
| M | DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3') | dna | 14 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, F, C, G
- 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.87 | 0.88 | 98 | empty |
| 2 | 429 | 0.84 | 0.92 | 43 | empty |
| 3 | 416 | 0.84 | 0.92 | 51 | empty |
| 4 | 694 | 0.81 | 0.85 | 56 | empty |
| 5 | 192 | 0.78 | 0.93 | 30 | empty |
Interfaces
28 interfaces between chains.
- A–B · 2113 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1991 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1757 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 853 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–F · 845 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6OES · Cryo-EM structure of mouse RAG1/2 stc complex (without nbd domain) · 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 0.99
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 6OES · PDBe 6OES · UniProt P15919 · UniProt P21784
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.