Research workbench
Cryo-electron microscopy structure of rag signal end complex (C2 symmetry)
Analyse Cryo-electron microscopy structure of rag signal end complex (C2 symmetry) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBX
- Type
- protein + DNA
- Length
- 1,918 residues
- Chains
- 12
- 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.-.-, 6.3.2.-
- UniProt
- O13033, Q1RLW7
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 6.3.2.-) | protein | 550 | 47% helix, 12% strand | O13033 |
| B, D | V(D)J recombination-activating protein 2 | protein | 351 | 1% helix, 42% strand | Q1RLW7 |
| E, H | 5'-D(*CP*AP*CP*AP*GP*TP*GP*CP*TP*AP*CP*AP*GP*AP*C)-3' | dna | 15 | — | — |
| F, G | 5'-D(P*GP*TP*CP*TP*GP*TP*AP*GP*CP*AP*CP*TP*GP*TP*G)-3' | dna | 15 | — | — |
| I, K | 5'-D(*GP*CP*GP*AP*TP*GP*GP*TP*TP*AP*AP*CP*CP*A)-3' | dna | 14 | — | — |
| J, L | 5'-D(P*TP*GP*GP*TP*TP*AP*AP*CP*CP*AP*TP*CP*GP*C)-3' | dna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, G, J, C, F, L
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.88 | 0.90 | 118 | empty |
| 2 | 1055 | 0.88 | 0.90 | 124 | empty |
| 3 | 595 | 0.82 | 0.88 | 66 | empty |
| 4 | 879 | 0.74 | 0.78 | 59 | empty |
| 5 | 661 | 0.73 | 0.80 | 52 | empty |
Interfaces
29 interfaces between chains.
- A–B · 2000 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1963 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1829 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 785 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 764 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3JBX · Cryo-electron microscopy structure of RAG Signal End Complex (C2 symmetry) · the same entry in another collection · chain L against L, TM-score 1.00
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 O13033
- Every structure of UniProt Q1RLW7
- Elsewhere: RCSB PDB 3JBX · PDBe 3JBX · UniProt O13033 · UniProt Q1RLW7
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