MolNFT v1 · #143891 · protein + DNA
I-onui K227Y, D236A bound to cognate substrate (pre-cleavage complex)
6BD0 · Ribosomal protein 3/HOMING endonuclease-like protein fusion: “I-onui K227Y, D236A bound to cognate substrate (pre-cleavage complex)”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.65). MolNFT v1 #143891 on…
- PDB
- 6BD0
- Type
- protein + DNA
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein 3/HOMING endonuclease-like protein fusion; DNA (25-mer)
- UniProt
- Q4VWW5
- Ligands
- CA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein 3/HOMING endonuclease-like protein fusion | protein | 300 | 49% helix, 23% strand | Q4VWW5 |
| B | DNA (25-mer) | dna | 25 | — | — |
| C | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.65 | 0.86 | 29 | empty |
| 2 | 200 | 0.60 | 0.82 | 30 | empty |
| 3 | 151 | 0.55 | 0.82 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1682 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 1574 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–C · 1186 Ų buried · 83 hydrogen bonds · nucleic-nucleic
Compared structures
- 6BD0 · I-OnuI K227Y, D236A 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 Q4VWW5
- Elsewhere: RCSB PDB 6BD0 · PDBe 6BD0 · UniProt Q4VWW5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.