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Crystal structure of hgfa in complex with the allosteric non- inhibitory antibody FAB40.DELTATRP and ac-kqlr-chloromethylketone
Analyse Crystal structure of hgfa in complex with the allosteric non- inhibitory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WUC
- Type
- protein
- Length
- 681 residues
- Chains
- 5
- 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
- ACE, NAG, 0QE
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 5 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 | 239 | 10% helix, 36% strand | Q04756 |
| B | Hepatocyte growth factor activator short chain (EC 3.4.21.-) | protein | 6 | 0% helix, 0% strand | Q04756 |
| H | Fab fragment FAB40.DELTATRP heavy chain | protein | 218 | 6% helix, 51% strand | — |
| I | ACE-kqlr-chloromethylketone inhibitor | protein | 4 | 0% helix, 25% strand | — |
| L | Fab fragment FAB40.DELTATRP light chain | protein | 214 | 5% helix, 51% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- 0QE · Chloromethane · ion · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.63 | 0.74 | 51 | empty |
| 2 | 225 | 0.58 | 0.80 | 39 | empty |
| 3 | 236 | 0.52 | 0.76 | 40 | empty |
| 4 | 136 | 0.50 | 0.80 | 28 | empty |
| 5 | 71 | 0.31 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1920 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 718 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 488 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 325 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, nonstandard).
Compared structures
- 2WUC · Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody… · 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 0.99
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 2WUC · PDBe 2WUC · UniProt Q04756
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