Research workbench
Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide
Analyse Crystal structure of the anti-human podoplanin antibody Fab fragment complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C94
- Type
- protein
- Length
- 901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.84
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- Light chain of Fab fragment; Heavy chain of Fab fragment; Peptide from Podoplanin
- UniProt
- Q86YL7
- Ligands
- SIA, A2G, GAL, PO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.84 · 5 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of Fab fragment | protein | 220 | 6% helix, 53% strand | — |
| B | Heavy chain of Fab fragment | protein | 223 | 4% helix, 52% strand | — |
| C, F | Peptide from Podoplanin | protein | 8 | 0% helix, 13% strand | Q86YL7 |
| D | Light chain of Fab fragment | protein | 219 | 6% helix, 49% strand | — |
| E | Heavy chain of Fab fragment | protein | 223 | 1% helix, 49% strand | — |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains B, A, C, E, D, F
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, C, F
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains E
- PO4 · Phosphate ion · ion · 4 copies · chains A, D, E
- GOL · Glycerol · additive · 7 copies · chains A, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.69 | 0.77 | 80 | GOL |
| 2 | 346 | 0.55 | 0.74 | 44 | GOL |
| 3 | 304 | 0.53 | 0.75 | 50 | PO4 |
| 4 | 92 | 0.45 | 0.80 | 20 | empty |
| 5 | 119 | 0.43 | 0.77 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1916 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1896 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 563 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 537 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 414 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 7C94 · Crystal structure of the anti-human podoplanin antibody Fab fragment complex with… · the same entry in another collection · chain E against E, TM-score 1.00
- Q86YL7 · AlphaFold monomer V2.0 prediction for podoplanin (Q86YL7) · a predicted model of the same protein · chain C against A, TM-score 0.40
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 Q86YL7
- Elsewhere: RCSB PDB 7C94 · PDBe 7C94 · UniProt Q86YL7
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