MolNFT v1 · #123034 · protein
Loop grafting onto a highly stable FN3 scaffold
5J7K · FN3CON-a-lys: “Loop grafting onto a highly stable FN3 scaffold”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.50). MolNFT v1 #123034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5J7K
- Type
- protein
- Length
- 607 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FN3CON-a-lys
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 8 distinct chains · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FN3CON-a-lys | protein | 84 | 0% helix, 51% strand | — |
| B | FN3CON-a-lys | protein | 90 | 0% helix, 48% strand | — |
| C | FN3CON-a-lys | protein | 78 | 0% helix, 55% strand | — |
| D | FN3CON-a-lys | protein | 54 | 0% helix, 39% strand | — |
| E | FN3CON-a-lys | protein | 73 | 0% helix, 53% strand | — |
| F | FN3CON-a-lys | protein | 79 | 0% helix, 54% strand | — |
| G | FN3CON-a-lys | protein | 85 | 0% helix, 53% strand | — |
| H | FN3CON-a-lys | protein | 64 | 0% helix, 41% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains B, G, A, C, D, F, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.50 | 0.81 | 15 | empty |
| 2 | 70 | 0.49 | 0.84 | 23 | empty |
| 3 | 134 | 0.39 | 0.74 | 23 | empty |
| 4 | 80 | 0.35 | 0.76 | 23 | empty |
Interfaces
9 interfaces between chains.
- B–G · 718 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 700 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 512 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 209 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5J7K · Loop grafting onto a highly stable FN3 scaffold · 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 5J7K · PDBe 5J7K
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