Research workbench
I-ltri E29D bound to cognate substrate (nicked complex)
Analyse I-ltri E29D bound to cognate substrate (nicked complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BCH
- Type
- protein + DNA
- Length
- 1,364 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like fusion protein; DNA…
- UniProt
- C7SWF3
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, H, L | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 289 | 50% helix, 20% strand | C7SWF3 |
| B, E, I, N | DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)- 3') | dna | 15 | — | — |
| C, F, J, O | DNA (26-mer) | dna | 26 | — | — |
| X, G, K, P | DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3') | dna | 11 | — | — |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.77 | 0.82 | 68 | empty |
| 2 | 756 | 0.76 | 0.81 | 61 | empty |
| 3 | 465 | 0.73 | 0.83 | 41 | empty |
| 4 | 402 | 0.73 | 0.84 | 34 | empty |
| 5 | 301 | 0.61 | 0.79 | 31 | empty |
Interfaces
32 interfaces between chains.
- D–F · 1376 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 1363 Ų buried · 19 hydrogen bonds · protein-nucleic
- L–O · 1363 Ų buried · 20 hydrogen bonds · protein-nucleic
- H–J · 1300 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 732 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6BCH · I-LtrI E29D bound to cognate substrate (nicked 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 6BCH · PDBe 6BCH · UniProt C7SWF3
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