MolNFT v2 · #177034 · protein
Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide
7C94: “Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide”. X-ray diffraction at 2.84, 4 ligands (SIA, A2G, GAL). MolNFT v2 #177034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
- UniProt
- Q86YL7
- Ligands
- SIA, A2G, GAL, PO4
Structure
x-ray diffraction · resolution 2.84 · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 220 | — | — |
| B | — | protein | 223 | — | — |
| C, F | — | protein | 8 | — | Q86YL7 |
| D | — | protein | 219 | — | — |
| E | — | protein | 223 | — | — |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains B, A, E, D, F
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains C, F
- GAL · beta-D-galactopyranose · sugar · 2 copies
- 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.
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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