MolNFT v1 · #111338 · protein
Crystal structure of monoclonal anti-human podoplanin antibody nz-1
4YNY · Heavy chain of antigen binding fragment, Fab: “Crystal structure of monoclonal anti-human podoplanin antibody nz-1”. X-ray diffraction, 10 pockets (best druggability 0.59). MolNFT v1 #111338 on GenesisL1: 3D structure, binding sites…
- PDB
- 4YNY
- Type
- protein
- Length
- 838 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of antigen binding fragment, Fab; Light chain of antigen binding fragment, Fab
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Heavy chain of antigen binding fragment, Fab | protein | 209 | 10% helix, 55% strand | — |
| B, D | Light chain of antigen binding fragment, Fab | protein | 210 | 8% helix, 53% strand | — |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.59 | 0.74 | 49 | empty |
| 2 | 496 | 0.58 | 0.73 | 59 | empty |
| 3 | 146 | 0.47 | 0.77 | 20 | empty |
| 4 | 142 | 0.46 | 0.77 | 19 | empty |
| 5 | 127 | 0.39 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1624 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1581 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 396 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 4YNY · Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 · 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
- Elsewhere: RCSB PDB 4YNY · PDBe 4YNY
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