MolNFT v1 · #163855 · protein

Crystal structure of the mab 15A in complex with comp-epitope P6

6SF6 · Comp-reactive monoclonal antibody 15A Fab fragment, heavy…: “Crystal structure of the mab 15A in complex with comp-epitope P6”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.72). MolNFT v1 #163855 on GenesisL1…

PDB: 6SF6
Type: protein
Length: 888 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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 · 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 H against H, 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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.