Research workbench
X-ray structure of furin in complex with the inhibitory antibody NB14
Analyse X-ray structure of furin in complex with the inhibitory antibody NB14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JMO
- Type
- protein
- Length
- 1,180 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Furin; Camelid vhh fragment; Cmk-inhibitor
- EC
- 3.4.21.75
- UniProt
- P09958
- Ligands
- DKA, NAG, CA, NA, 0QE
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Furin (EC 3.4.21.75) | protein | 469 | 21% helix, 28% strand | P09958 |
| B | Furin (EC 3.4.21.75) | protein | 471 | 21% helix, 28% strand | P09958 |
| C | Camelid vhh fragment | protein | 115 | 8% helix, 46% strand | — |
| D | Camelid vhh fragment | protein | 117 | 5% helix, 47% strand | — |
| G, H | Cmk-inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- DKA · Decanoic acid · ligand · 2 copies · chains A, G, B, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, G, B, H
- NA · Sodium ion · metal · 2 copies · chains A, B
- 0QE · Chloromethane · ion · 2 copies · chains A, G, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.71 | 0.98 | 18 | empty |
| 2 | 64 | 0.57 | 0.89 | 19 | empty |
| 3 | 140 | 0.50 | 0.79 | 18 | empty |
| 4 | 106 | 0.49 | 0.81 | 18 | empty |
| 5 | 142 | 0.47 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 760 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 736 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 727 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 520 Ų buried · 22 hydrogen bonds · protein-protein
- B–H · 518 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan, 2 covalent, 2 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
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 5JMO · PDBe 5JMO · UniProt P09958
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