Research workbench
Wild-type I-onui bound to A3G substrate (post-cleavage complex)
Analyse Wild-type I-onui bound to A3G substrate (post-cleavage complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BDA
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like protein fusion; Cleaved cognate DNA strand…
- UniProt
- Q4VWW5
- Ligands
- MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/HOMING endonuclease-like protein fusion | protein | 295 | 50% helix, 23% strand | Q4VWW5 |
| B | Cleaved cognate DNA strand, +11 sense | dna | 14 | — | — |
| C | Cleaved cognate DNA strand, -11 sense | dna | 11 | — | — |
| D | Cleaved cognate DNA strand, -11 antisense | dna | 15 | — | — |
| E | Cleaved cognate DNA strand, +11 antisense | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.70 | 0.96 | 20 | empty |
| 2 | 285 | 0.64 | 0.81 | 42 | MG |
| 3 | 108 | 0.42 | 0.77 | 23 | empty |
| 4 | 55 | 0.26 | 0.74 | 12 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1151 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 1013 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 629 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–E · 621 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 560 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 6BDA · Wild-type I-OnuI bound to A3G substrate (post-cleavage complex) · the same entry in another collection · chain A against A, 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 Q4VWW5
- Elsewhere: RCSB PDB 6BDA · PDBe 6BDA · UniProt Q4VWW5
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