Research workbench
Crystal structure of hgfa in complex with the allosteric inhibitory antibody FAB40
Analyse Crystal structure of hgfa in complex with the allosteric inhibitory antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K2U
- Type
- protein
- Length
- 661 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor activator long chain; Hepatocyte growth factor activator short…
- EC
- 3.4.21.-
- UniProt
- Q04756
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor activator long chain (EC 3.4.21.-) | protein | 233 | 10% helix, 35% strand | Q04756 |
| B | Hepatocyte growth factor activator short chain (EC 3.4.21.-) | protein | 5 | 0% helix, 0% strand | Q04756 |
| H | Antibody, Fab fragment, heavy chain | protein | 215 | 7% helix, 52% strand | — |
| L | Antibody, Fab fragment, light chain | protein | 208 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.57 | 0.77 | 33 | empty |
| 2 | 400 | 0.56 | 0.74 | 45 | empty |
| 3 | 295 | 0.56 | 0.76 | 53 | empty |
| 4 | 101 | 0.55 | 0.84 | 23 | empty |
| 5 | 66 | 0.30 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1722 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 759 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 373 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3K2U · Crystal structure of HGFA in complex with the allosteric inhibitory antibody Fab40 · the same entry in another collection · chain A against A, TM-score 1.00
- Q04756 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor activator (Q04756) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q04756
- Elsewhere: RCSB PDB 3K2U · PDBe 3K2U · UniProt Q04756
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