MolNFT v1 · #17931 · protein
Crystal structure of the proprotein convertase furin
1P8J · Furin precursor: “Crystal structure of the proprotein convertase furin”. X-ray diffraction, 10 ligands (DKA, NAG, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #17931 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1P8J
- Type
- protein
- Length
- 3,772 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Furin precursor; Decanoyl-arg-val-lys-arg-chloromethylketone inhibitor
- EC
- 3.4.21.75
- UniProt
- P23188
- Ligands
- DKA, NAG, BMA, MAN, GAL, FUL, FUC, CA, SO4, 0QE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Furin precursor (EC 3.4.21.75) | protein | 470 | 20% helix, 29% strand | P23188 |
| B | Furin precursor (EC 3.4.21.75) | protein | 468 | 21% helix, 29% strand | P23188 |
| C, D, E, G | Furin precursor (EC 3.4.21.75) | protein | 467 | 21% helix, 29% strand | P23188 |
| F | Furin precursor (EC 3.4.21.75) | protein | 468 | 21% helix, 28% strand | P23188 |
| H | Furin precursor (EC 3.4.21.75) | protein | 466 | 21% helix, 28% strand | P23188 |
| J, K, L, M, N, P, Q, R | Decanoyl-arg-val-lys-arg-chloromethylketone inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- DKA · Decanoic acid · ligand · 8 copies · chains A, D, J, B, K, C, L, M, E, F, N, P, G, H, Q, R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, G, B, E, F, H
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies
- FUL · beta-L-fucopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains G
- CA · Calcium ion · metal · 16 copies · chains A, J, B, K, C, L, D, M, E, N, F, P, G, Q, H, R
- SO4 · Sulfate ion · ion · 70 copies · chains A, J, C, B, D, L, M, E, N, H, F, G, Q, K, P, R
- 0QE · Chloromethane · ion · 8 copies · chains A, J, B, K, C, L, D, M, E, N, F, P, G, Q, H, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.82 | 0.84 | 142 | empty |
| 2 | 371 | 0.78 | 0.88 | 47 | SO4 |
| 3 | 512 | 0.77 | 0.84 | 55 | SO4 |
| 4 | 425 | 0.77 | 0.86 | 50 | SO4 |
| 5 | 382 | 0.75 | 0.86 | 42 | empty |
Interfaces
26 interfaces between chains.
- F–G · 1638 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1630 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1576 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 1545 Ų buried · 12 hydrogen bonds · protein-protein
- G–Q · 535 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 8 covalent, 8 glycan, 8 modified (disulfide, covalent ligand, N-glycosylation, nonstandard).
Compared structures
- 1P8J · Crystal structure of the proprotein convertase furin · the same entry in another collection · chain R against R, 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 P23188
- Elsewhere: RCSB PDB 1P8J · PDBe 1P8J · UniProt P23188
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