Research workbench
Bbragl-3'TIR synaptic complex with nicked DNA refined with C2 symmetry
Analyse Bbragl-3'TIR synaptic complex with nicked DNA refined with C2 symmetry in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B40
- Type
- protein + DNA
- Length
- 1,938 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAG1L,RAG1L; 31TIR intact strand; 31TIR pre-nicked strand of signal DNA; 31TIR pre-nicked…
- UniProt
- A0A185KID9, A0A185KIE0
- Ligands
- CA, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 20% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | RAG1L,RAG1L | protein | 553 | 34% helix, 8% strand | A0A185KID9 |
| B, F | 31TIR intact strand | dna | 25 | — | — |
| C, G | 31TIR pre-nicked strand of signal DNA | dna | 13 | — | — |
| D, H | 31TIR pre-nicked strand of flanking DNA | dna | 12 | — | — |
| M, N | RAG2L | protein | 366 | 0% helix, 23% strand | A0A185KIE0 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, E, F
- ZN · Zinc ion · metal · 2 copies · chains A, E
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 | 856 | 0.86 | 0.88 | 128 | empty |
| 2 | 790 | 0.85 | 0.88 | 56 | empty |
| 3 | 634 | 0.81 | 0.86 | 66 | empty |
| 4 | 323 | 0.80 | 0.90 | 62 | empty |
| 5 | 654 | 0.77 | 0.83 | 57 | empty |
Interfaces
21 interfaces between chains.
- A–E · 1507 Ų buried · 9 hydrogen bonds · protein-protein
- A–M · 1357 Ų buried · 6 hydrogen bonds · protein-protein
- E–N · 1352 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1156 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 1153 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 6B40 · BbRAGL-3'TIR synaptic complex with nicked DNA refined with C2 symmetry · the same entry in another collection · chain H against H, 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 A0A185KID9
- Every structure of UniProt A0A185KIE0
- Elsewhere: RCSB PDB 6B40 · PDBe 6B40 · UniProt A0A185KID9 · UniProt A0A185KIE0
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