Research workbench
I-LtrI E184D bound to cognate substrate (pre-cleavage complex)
Analyse I-LtrI E184D 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
- 6BCN
- Type
- protein + DNA
- Length
- 1,368 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Leptographium truncatum; SYNTHETIC CONSTRUCT
- Molecule
- Ribosomal protein 3/homing endonuclease-like fusion protein; DNA (26-mer)
- UniProt
- C7SWF3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.5 · 5 distinct chains · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/homing endonuclease-like fusion protein | protein | 291 | 51% helix, 21% strand | C7SWF3 |
| C, G, J | Ribosomal protein 3/homing endonuclease-like fusion protein | protein | 290 | 51% helix, 21% strand | C7SWF3 |
| B, E, H, K | DNA (26-mer) | dna | 26 | — | — |
| D | DNA (26-mer) | dna | 25 | — | — |
| F, I, L | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains A, B, D, C, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.68 | 0.91 | 24 | CA |
| 2 | 114 | 0.66 | 0.90 | 23 | CA |
| 3 | 184 | 0.61 | 0.83 | 28 | empty |
| 4 | 182 | 0.58 | 0.82 | 30 | empty |
| 5 | 151 | 0.54 | 0.82 | 24 | empty |
Interfaces
22 interfaces between chains.
- C–E · 1614 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–B · 1588 Ų buried · 46 hydrogen bonds · protein-nucleic
- A–D · 1566 Ų buried · 36 hydrogen bonds · protein-nucleic
- J–K · 1558 Ų buried · 48 hydrogen bonds · protein-nucleic
- G–H · 1535 Ų buried · 44 hydrogen bonds · protein-nucleic
Compared structures
- 6BCN · I-ltri E184D 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 6BCN · PDBe 6BCN · UniProt C7SWF3
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