Research workbench
Crystal structure of onartuzumab Fab in complex with met and hgf-beta
Analyse Crystal structure of onartuzumab Fab in complex with met and hgf-beta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3J
- Type
- protein
- Length
- 1,164 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor; Hepatocyte growth factor beta chain; Onartuzumab Fab heavy…
- EC
- 2.7.10.1
- UniProt
- P14210, P08581
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 227 | 11% helix, 37% strand | P14210 |
| B | Hepatocyte growth factor beta chain (EC 2.7.10.1) | protein | 499 | 8% helix, 43% strand | P08581 |
| H | Onartuzumab Fab heavy chain | protein | 221 | 5% helix, 51% strand | — |
| L | Onartuzumab Fab light chain | protein | 217 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.71 | 0.77 | 56 | empty |
| 2 | 818 | 0.70 | 0.76 | 70 | empty |
| 3 | 127 | 0.67 | 0.89 | 33 | empty |
| 4 | 531 | 0.61 | 0.75 | 61 | empty |
| 5 | 202 | 0.56 | 0.79 | 32 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1840 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 950 Ų buried · 21 hydrogen bonds · protein-protein
- B–H · 551 Ų buried · 14 hydrogen bonds · protein-protein
- B–L · 499 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4K3J · Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta · the same entry in another collection · chain A against A, TM-score 1.00
- P14210 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (P14210) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P14210
- Every structure of UniProt P08581
- Elsewhere: RCSB PDB 4K3J · PDBe 4K3J · UniProt P14210 · UniProt P08581
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.