Research workbench
Cryo-EM structure of mouse RAG1/2 stc complex
Analyse Cryo-EM structure of mouse RAG1/2 stc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OET
- Type
- protein + DNA
- Length
- 2,134 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; DNA…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784
- Ligands
- CA, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 9 distinct chains · 31% 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 | 618 | 46% helix, 11% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 342 | 3% helix, 48% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 623 | 47% helix, 10% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 343 | 3% helix, 48% strand | P21784 |
| F | DNA (50-mer) | dna | 50 | — | — |
| I, J | DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)- 3') | dna | 15 | — | — |
| G | DNA (59-mer) | dna | 59 | — | — |
| L | DNA (30-mer) | dna | 30 | — | — |
| M | DNA (39-mer) | dna | 39 | — | — |
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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.82 | 0.91 | 50 | empty |
| 2 | 674 | 0.81 | 0.86 | 55 | empty |
| 3 | 271 | 0.81 | 0.93 | 53 | CA |
| 4 | 674 | 0.81 | 0.85 | 57 | empty |
| 5 | 277 | 0.81 | 0.93 | 37 | empty |
Interfaces
28 interfaces between chains.
- A–C · 4100 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2082 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1983 Ų buried · 45 hydrogen bonds · protein-protein
- G–M · 1727 Ų buried · 132 hydrogen bonds · nucleic-nucleic
- C–F · 1484 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
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 6OET · PDBe 6OET · UniProt P15919 · UniProt P21784
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