MolNFT v1 · #122100 · protein
Structure of a computationally designed 17-ohp binder
5IF6 · OHP9_1C: “Structure of a computationally designed 17-ohp binder”. X-ray diffraction, 2 ligands (3QZ, NA), 8 pockets (best druggability 0.78). MolNFT v1 #122100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IF6
- Type
- protein
- Length
- 800 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OHP9_1C
- Ligands
- 3QZ, NA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | OHP9_1C | protein | 134 | 26% helix, 42% strand | — |
| B | OHP9_1C | protein | 133 | 26% helix, 41% strand | — |
| F | OHP9_1C | protein | 131 | 27% helix, 40% strand | — |
Ligands and binding sites
- 3QZ · (9beta)-17-hydroxypregn-4-ene-3,20-dione · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.78 | 0.86 | 48 | 3QZ, NA |
| 2 | 993 | 0.78 | 0.80 | 85 | 3QZ |
| 3 | 386 | 0.77 | 0.86 | 43 | 3QZ |
| 4 | 360 | 0.76 | 0.86 | 42 | 3QZ, NA |
| 5 | 368 | 0.75 | 0.85 | 45 | 3QZ, NA |
Interfaces
4 interfaces between chains.
- A–E · 980 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 400 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 331 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5IF6 · Structure of a computationally designed 17-OHP binder · 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 5IF6 · PDBe 5IF6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.