MolNFT v1 · #186393 · protein + DNA
Fourth stage reengineered variant of I-onui with stability enhancing substitutions
7RCF · I-ONUI_E-HPD1-E: “Fourth stage reengineered variant of I-onui with stability enhancing substitutions”. X-ray diffraction, 3 ligands (CA, NA, CL), 7 pockets (best druggability 0.69). MolNFT v1 #186393 on GenesisL1: 3D structure…
- PDB
- 7RCF
- Type
- protein + DNA
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ONUI_E-HPD1-E; DNA (26-mer)
- Ligands
- CA, NA, CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | I-ONUI_E-HPD1-E | protein | 290 | 52% helix, 21% strand | — |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.69 | 0.96 | 22 | empty |
| 2 | 55 | 0.61 | 0.92 | 20 | empty |
| 3 | 195 | 0.57 | 0.81 | 29 | empty |
| 4 | 120 | 0.49 | 0.81 | 26 | empty |
| 5 | 106 | 0.43 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1560 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–B · 1371 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–C · 1292 Ų buried · 108 hydrogen bonds · nucleic-nucleic
Compared structures
- 7RCF · Fourth stage reengineered variant of I-OnuI with stability enhancing substitutions · 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
- Elsewhere: RCSB PDB 7RCF · PDBe 7RCF
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.