MolNFT v1 · #143876 · protein + DNA
I-ltri A28G bound to cognate substrate (pre-cleavage complex)
6BCG · Ribosomal protein 3/HOMING endonuclease-like fusion protein: “I-ltri A28G bound to cognate substrate (pre-cleavage complex)”. X-ray diffraction, 1 ligand (CA), 18 pockets (best druggability 0.77). MolNFT v1 #143876 on GenesisL1: 3D…
- PDB
- 6BCG
- Type
- protein + DNA
- Length
- 1,340 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
- 18 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 287 | 51% helix, 21% strand | C7SWF3 |
| E, B, H, K | DNA (26-mer) | dna | 26 | — | — |
| F, C, I, L | DNA (26-mer) | dna | 26 | — | — |
| A | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 282 | 51% helix, 21% strand | C7SWF3 |
| G | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 281 | 53% helix, 21% strand | C7SWF3 |
| J | Ribosomal protein 3/HOMING endonuclease-like fusion protein | protein | 282 | 53% helix, 21% strand | C7SWF3 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains D, E, F, A, B, C, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.77 | 0.80 | 92 | CA |
| 2 | 699 | 0.74 | 0.80 | 60 | CA |
| 3 | 275 | 0.68 | 0.84 | 25 | empty |
| 4 | 94 | 0.67 | 0.91 | 23 | empty |
| 5 | 269 | 0.64 | 0.82 | 26 | empty |
Interfaces
19 interfaces between chains.
- A–C · 1454 Ų buried · 27 hydrogen bonds · protein-nucleic
- D–F · 1423 Ų buried · 24 hydrogen bonds · protein-nucleic
- J–L · 1418 Ų buried · 20 hydrogen bonds · protein-nucleic
- G–I · 1414 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–E · 1395 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- 6BCG · I-LtrI A28G 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 6BCG · PDBe 6BCG · UniProt C7SWF3
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