Research workbench
Crystal structure of antibody 14A in complex with MUC1 GLYCOPEPTIDE(GLYCOST)
Analyse Crystal structure of antibody 14A in complex with MUC1 GLYCOPEPTIDE(GLYCOST) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VAC
- Type
- protein
- Length
- 1,319 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14A Fab light chain; 14A Fab heavy chain; Mucin-1 subunit alpha
- UniProt
- P15941
- Ligands
- NGA
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14A Fab light chain | protein | 217 | 7% helix, 52% strand | — |
| B | 14A Fab heavy chain | protein | 219 | 8% helix, 53% strand | — |
| C | 14A Fab light chain | protein | 214 | 7% helix, 53% strand | — |
| D | 14A Fab heavy chain | protein | 217 | 8% helix, 53% strand | — |
| E | 14A Fab light chain | protein | 215 | 7% helix, 53% strand | — |
| F | 14A Fab heavy chain | protein | 211 | 9% helix, 54% strand | — |
| G, H | Mucin-1 subunit alpha | protein | 9 | 0% helix, 11% strand | P15941 |
| I | Mucin-1 subunit alpha | protein | 8 | 0% helix, 0% strand | P15941 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 6 copies · chains B, G, D, H, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.73 | 0.76 | 110 | empty |
| 2 | 665 | 0.68 | 0.77 | 50 | empty |
| 3 | 608 | 0.66 | 0.76 | 54 | empty |
| 4 | 320 | 0.55 | 0.75 | 38 | empty |
| 5 | 211 | 0.52 | 0.77 | 29 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1953 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1902 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1799 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 669 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 608 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 5 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 7VAC · PDBe 7VAC · UniProt P15941
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