MolNFT v1 · #126098 · protein
107_A07 Fab in complex with fragment of the met receptor
5LSP · Hepatocyte growth factor receptor: “107_A07 Fab in complex with fragment of the met receptor”. X-ray diffraction, 1 ligand (NAG), 15 pockets (best druggability 0.79). MolNFT v1 #126098 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LSP
- Type
- protein
- Length
- 1,319 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor receptor; 107_A07 Fab heavy chain; 107_A07 Fab light chain
- EC
- 2.7.10.1
- UniProt
- P08581
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 222 | 7% helix, 51% strand | P08581 |
| H, S | 107_A07 Fab heavy chain | protein | 216 | 7% helix, 51% strand | — |
| L, T | 107_A07 Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| X | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 9 | 78% helix, 0% strand | P08581 |
| Y | Hepatocyte growth factor receptor (EC 2.7.10.1) | protein | 10 | 80% helix, 0% strand | P08581 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.79 | 0.95 | 35 | empty |
| 2 | 637 | 0.71 | 0.79 | 68 | empty |
| 3 | 237 | 0.57 | 0.78 | 35 | empty |
| 4 | 243 | 0.54 | 0.76 | 36 | empty |
| 5 | 192 | 0.50 | 0.77 | 33 | empty |
Interfaces
14 interfaces between chains.
- H–L · 1815 Ų buried · 12 hydrogen bonds · protein-protein
- S–T · 1781 Ų buried · 12 hydrogen bonds · protein-protein
- P–S · 519 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 518 Ų buried · 18 hydrogen bonds · protein-protein
- H–T · 449 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5LSP · 107_A07 Fab in complex with fragment of the Met receptor · the same entry in another collection · chain A against A, TM-score 1.00
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 P08581
- Elsewhere: RCSB PDB 5LSP · PDBe 5LSP · UniProt P08581
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.