Research workbench
I-ltri E184D bound to non-cognate C4 substrate (pre-cleavage complex)
Analyse I-ltri E184D bound to non-cognate C4 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
- 6BCT
- 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 (26-mer); DNA (27-mer)
- UniProt
- C7SWF3
- Ligands
- CA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 290 | 49% helix, 20% strand | C7SWF3 |
| B | DNA (26-mer) | dna | 26 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.66 | 0.85 | 30 | empty |
| 2 | 238 | 0.56 | 0.79 | 23 | empty |
| 3 | 87 | 0.55 | 0.86 | 21 | empty |
| 4 | 58 | 0.45 | 0.84 | 15 | empty |
| 5 | 69 | 0.40 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1445 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 1435 Ų buried · 40 hydrogen bonds · protein-nucleic
- B–D · 1293 Ų buried · 111 hydrogen bonds · nucleic-nucleic
Compared structures
- 6BCT · I-LtrI E184D bound to non-cognate C4 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 6BCT · PDBe 6BCT · UniProt C7SWF3
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