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Short form hgfa with inhibitory FAB75
Analyse Short form hgfa with inhibitory FAB75 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R0L
- Type
- protein
- Length
- 683 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain, Fab portion only; Hepatocyte growth factor…
- EC
- 3.4.21.-
- UniProt
- Q04756
- Ligands
- NAG, BMA
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody light chain | protein | 214 | 7% helix, 51% strand | — |
| H | Antibody heavy chain, Fab portion only | protein | 220 | 9% helix, 51% strand | — |
| A | Hepatocyte growth factor activator (EC 3.4.21.-) | protein | 239 | 11% helix, 36% strand | Q04756 |
| B | Hepatocyte growth factor activator | protein | 10 | 0% helix, 0% strand | Q04756 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.62 | 0.80 | 40 | empty |
| 2 | 422 | 0.56 | 0.74 | 56 | empty |
| 3 | 242 | 0.51 | 0.75 | 43 | empty |
| 4 | 79 | 0.42 | 0.80 | 16 | empty |
| 5 | 87 | 0.35 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1943 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 790 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 467 Ų buried · 4 hydrogen bonds · protein-protein
- L–A · 306 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
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 Q04756
- Elsewhere: RCSB PDB 2R0L · PDBe 2R0L · UniProt Q04756
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