Research workbench

Crystal structure of the mAb 15A in complex with COMP-epitope P6

Analyse Crystal structure of the mAb 15A in complex with COMP-epitope P6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SF6
Type: protein
Length: 888 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.9
Source: Mus musculus; SYNTHETIC CONSTRUCT
Molecule: COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain; COMP-reactive monoclonal…
Ligands: SO4
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · resolution 1.9 · 4 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain	protein	216	8% helix, 52% strand	—
L	COMP-reactive monoclonal antibody 15A Fab fragment, light chain	protein	216	6% helix, 52% strand	—
B	COMP-reactive monoclonal antibody 15A Fab fragment, light chain	protein	218	6% helix, 52% strand	—
C, D	P6 epitope of cartilage oligomeric matrix protein (COMP)	protein	11	0% helix, 18% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains H, L, C
GOL · Glycerol · additive · 6 copies · chains H, L, A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	849	0.72	0.77	100	GOL
2	679	0.63	0.73	69	empty
3	65	0.46	0.83	23	empty
4	82	0.45	0.81	24	empty
5	149	0.42	0.75	18	GOL

Interfaces

9 interfaces between chains.

H–L · 1808 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1778 Å² buried · 16 hydrogen bonds · protein-protein
H–C · 470 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 430 Å² buried · 11 hydrogen bonds · protein-protein
H–A · 372 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, oxidation).

Compared structures

6SF6 · Crystal structure of the mab 15A in complex with comp-epitope P6 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6SF6 · PDBe 6SF6

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