MolNFT v1 · #53427 · protein
Crystal structure of hgfa in complex with the allosteric non- inhibitory antibody FAB40.DELTATRP
2WUB · Hepatocyte growth factor activator long chain: “Crystal structure of hgfa in complex with the allosteric non- inhibitory antibody FAB40.DELTATRP”. X-ray diffraction, 2 ligands (NAG, BMA), 16 pockets (best druggability 0.58). MolNFT…
- PDB
- 2WUB
- Type
- protein
- Length
- 1,316 residues
- Chains
- 8
- 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, BMA
- Pockets
- 16 · best druggability 0.58
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor activator long chain (EC 3.4.21.-) | protein | 231 | 10% helix, 35% strand | Q04756 |
| B | Hepatocyte growth factor activator short chain (EC 3.4.21.-) | protein | 6 | 0% helix, 0% strand | Q04756 |
| C | Hepatocyte growth factor activator long chain (EC 3.4.21.-) | protein | 228 | 10% helix, 35% strand | Q04756 |
| D | Hepatocyte growth factor activator short chain (EC 3.4.21.-) | protein | 5 | 0% helix, 0% strand | Q04756 |
| H | Fab fragment FAB40.DELTATRP heavy chain | protein | 213 | 12% helix, 50% strand | — |
| L, Q | Fab fragment FAB40.DELTATRP light chain | protein | 214 | 7% helix, 49% strand | — |
| R | Fab fragment FAB40.DELTATRP heavy chain | protein | 205 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.58 | 0.80 | 36 | empty |
| 2 | 234 | 0.54 | 0.77 | 42 | empty |
| 3 | 191 | 0.52 | 0.78 | 29 | empty |
| 4 | 227 | 0.52 | 0.76 | 39 | empty |
| 5 | 278 | 0.51 | 0.74 | 39 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1816 Ų buried · 16 hydrogen bonds · protein-protein
- Q–R · 1688 Ų buried · 11 hydrogen bonds · protein-protein
- C–R · 733 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 702 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 446 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2WUB · Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody… · the same entry in another collection · chain R against R, TM-score 1.00
- Q04756 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor activator (Q04756) · a predicted model of the same protein · chain C 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 2WUB · PDBe 2WUB · UniProt Q04756
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