Research workbench
I-ltri G183A bound to cognate substrate (pre-cleavage complex)
Analyse I-ltri G183A 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
- 6BCF
- Type
- protein + DNA
- Length
- 1,361 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like fusion protein; DNA (26-mer)
- UniProt
- C7SWF3
- Ligands
- CA
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, G | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 288 | 52% helix, 21% strand | C7SWF3 |
| E, B, H, K | DNA (26-mer) | dna | 26 | — | — |
| F, C, I, L | DNA (26-mer) | dna | 26 | — | — |
| J | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 289 | 52% helix, 21% strand | C7SWF3 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains D, E, F, A, B, C, G, I, H, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.76 | 0.82 | 65 | CA |
| 2 | 654 | 0.75 | 0.81 | 53 | CA |
| 3 | 590 | 0.73 | 0.81 | 56 | CA |
| 4 | 609 | 0.72 | 0.80 | 55 | CA |
| 5 | 50 | 0.61 | 0.94 | 16 | empty |
Interfaces
19 interfaces between chains.
- G–I · 1357 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 1336 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–F · 1331 Ų buried · 18 hydrogen bonds · protein-nucleic
- G–H · 1309 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1307 Ų buried · 27 hydrogen bonds · protein-nucleic
Compared structures
- 6BCF · I-LtrI G183A bound to cognate substrate (pre-cleavage complex) · the same entry in another collection · chain D against D, 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 6BCF · PDBe 6BCF · UniProt C7SWF3
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