Research workbench
Wild-type I-ltri bound to cognate substrate (pre-cleavage complex)
Analyse Wild-type I-ltri bound to cognate substrate (pre-cleavage complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BCE
- Type
- protein + DNA
- Length
- 343 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like fusion protein; DNA (27-mer)
- UniProt
- C7SWF3
- Ligands
- CA
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 289 | 52% helix, 21% strand | C7SWF3 |
| B | DNA (27-mer) | dna | 27 | — | — |
| C | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
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 | 107 | 0.70 | 0.93 | 22 | empty |
| 2 | 187 | 0.52 | 0.79 | 28 | empty |
| 3 | 52 | 0.41 | 0.83 | 15 | empty |
| 4 | 58 | 0.35 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1604 Ų buried · 46 hydrogen bonds · protein-nucleic
- A–C · 1520 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–C · 1311 Ų buried · 106 hydrogen bonds · nucleic-nucleic
Compared structures
- 6BCE · Wild-type I-LtrI bound to cognate substrate (pre-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 C7SWF3
- Elsewhere: RCSB PDB 6BCE · PDBe 6BCE · UniProt C7SWF3
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