Research workbench
X-ray structure of human furin in complex with the competitive inhibitor meta-guanidinomethyl-phac-rvr-amba
Analyse X-ray structure of human furin in complex with the competitive inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OMC
- Type
- protein
- Length
- 2,810 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Furin; Meta-guanidinomethyl-phenylacetyl-arg-val-arg- (AMIDOMETHYL)BENZAMIDINE
- EC
- 3.4.21.75
- UniProt
- P09958
- Ligands
- 2UC, 00S, CA, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Furin (EC 3.4.21.75) | protein | 466 | 21% helix, 28% strand | P09958 |
| B, D, E, F | Furin (EC 3.4.21.75) | protein | 465 | 21% helix, 28% strand | P09958 |
| H, I, J, K, L, N | Meta-guanidinomethyl-phenylacetyl-arg-val-arg- (AMIDOMETHYL)BENZAMIDINE | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 2UC · 1-[3-(2-oxoethyl)benzyl]guanidine · ligand · 6 copies · chains A, H, B, I, C, J, D, K, E, L, F, N
- 00S · 4-(aminomethyl)benzenecarboximidamide · ligand · 6 copies · chains A, H, B, I, C, J, D, K, E, L, F, N
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 24 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.80 | 0.87 | 54 | FMT |
| 2 | 508 | 0.80 | 0.87 | 50 | FMT |
| 3 | 757 | 0.79 | 0.83 | 85 | FMT |
| 4 | 695 | 0.78 | 0.82 | 90 | FMT |
| 5 | 697 | 0.77 | 0.82 | 96 | FMT |
Interfaces
11 interfaces between chains.
- A–B · 1368 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1354 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1337 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1074 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 covalent (disulfide, covalent ligand).
Compared structures
- 4OMC · X-ray structure of human furin in complex with the competitive inhibitor… · the same entry in another collection · chain N against N, 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 P09958
- Elsewhere: RCSB PDB 4OMC · PDBe 4OMC · UniProt P09958
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