Research workbench
Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS)
Analyse Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VAZ
- Type
- protein
- Length
- 1,310 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.73
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- 14A fab light chain; 14A fab heavy chain; Mucin-1 subunit alpha
- UniProt
- P15941
- Ligands
- NGA
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.73 · 8 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 14A fab light chain | protein | 215 | 8% helix, 52% strand | — |
| D | 14A fab heavy chain | protein | 213 | 10% helix, 54% strand | — |
| G, E | Mucin-1 subunit alpha | protein | 10 | 0% helix, 0% strand | P15941 |
| A | 14A fab light chain | protein | 213 | 8% helix, 53% strand | — |
| B | 14A fab heavy chain | protein | 216 | 9% helix, 53% strand | — |
| F | 14A fab light chain | protein | 216 | 7% helix, 52% strand | — |
| H | 14A fab heavy chain | protein | 210 | 9% helix, 53% strand | — |
| I | Mucin-1 subunit alpha | protein | 7 | 0% helix, 0% strand | P15941 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.70 | 0.76 | 77 | empty |
| 2 | 797 | 0.70 | 0.76 | 75 | empty |
| 3 | 692 | 0.66 | 0.75 | 83 | empty |
| 4 | 270 | 0.53 | 0.75 | 45 | empty |
| 5 | 63 | 0.49 | 0.85 | 20 | empty |
Interfaces
11 interfaces between chains.
- F–H · 1914 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1882 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1788 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 375 Ų buried · 4 hydrogen bonds · protein-protein
- D–G · 363 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
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 P15941
- Elsewhere: RCSB PDB 7VAZ · PDBe 7VAZ · UniProt P15941
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