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Crystal structure of antibody 14A in complex with MUC1 GLYCOPEPTIDE(GLYCOT)

Analyse Crystal structure of antibody 14A in complex with MUC1 GLYCOPEPTIDE(GLYCOT) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V8Q
Type: protein
Length: 1,326 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: 16 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	14A Fab light chain	protein	217	7% helix, 50% strand	—
B	14A Fab heavy chain	protein	219	8% helix, 52% strand	—
D	14A Fab heavy chain	protein	218	8% helix, 53% strand	—
E	14A Fab light chain	protein	215	7% helix, 53% strand	—
F	14A Fab heavy chain	protein	215	10% helix, 53% strand	—
G, I	Mucin-1 subunit alpha	protein	8	0% helix, 0% strand	P15941
H	Mucin-1 subunit alpha	protein	9	0% helix, 0% strand	P15941

Ligands and binding sites

NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains B, G, D, H, F, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.74	0.77	104	empty
2	641	0.70	0.78	54	empty
3	660	0.69	0.77	59	empty
4	310	0.58	0.77	36	empty
5	325	0.55	0.75	35	empty

Interfaces

12 interfaces between chains.

C–D · 2016 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1941 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1875 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 663 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 605 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 1 glycan (disulfide, O-glycosylation).

Compared structures

7V8Q · Crystal structure of antibody 14A in complex with MUC1 Glycopeptide(GlycoT) · the same entry in another collection · chain I against I, TM-score 1.00
P15941 · AlphaFold monomer V2.0 prediction for mucin-1 (P15941) · a predicted model of the same protein · chain G against A, TM-score 0.51

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 7V8Q · PDBe 7V8Q · UniProt P15941

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