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Crystal structure of broadly neutralizing antibody HEPC3

Analyse Crystal structure of broadly neutralizing antibody HEPC3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MED
Type: protein
Length: 1,305 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody HEPC3 heavy chain; Antibody HEPC3 light chain
Ligands: SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody HEPC3 heavy chain	protein	219	8% helix, 53% strand	—
B, I	Antibody HEPC3 light chain	protein	213	6% helix, 51% strand	—
C	Antibody HEPC3 heavy chain	protein	226	9% helix, 51% strand	—
D	Antibody HEPC3 light chain	protein	212	6% helix, 51% strand	—
G	Antibody HEPC3 heavy chain	protein	222	9% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, I

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

Pockets

14 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	1018	0.84	0.85	112	empty
2	202	0.65	0.85	39	empty
3	675	0.65	0.74	60	empty
4	638	0.62	0.74	66	empty
5	51	0.59	0.92	21	empty

Interfaces

9 interfaces between chains.

C–D · 2065 Å² buried · 23 hydrogen bonds · protein-protein
G–I · 1880 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1827 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 581 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 383 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide (disulfide).

Compared structures

6MED · Crystal structure of broadly neutralizing antibody HEPC3 · the same entry in another collection · chain C against C, 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 6MED · PDBe 6MED

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