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Crystal structure of human monoclonal antibody H7.200 in complex with H7N9 hemagglutinin HA1

Analyse Crystal structure of human monoclonal antibody H7.200 in complex with H7N9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UIG
Type: protein
Length: 1,395 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin; H7.200 Fab heavy chain; H7.200 Fab light chain
UniProt: A0A4Y5QYN9
Ligands: NAG
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, A	Hemagglutinin	protein	269	10% helix, 39% strand	A0A4Y5QYN9
H	H7.200 Fab heavy chain	protein	217	5% helix, 52% strand	—
L	H7.200 Fab light chain	protein	212	5% helix, 50% strand	—
B	H7.200 Fab heavy chain	protein	218	6% helix, 52% strand	—
C	H7.200 Fab light chain	protein	210	6% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G, A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.63	0.74	67	empty
2	560	0.61	0.74	58	empty
3	165	0.59	0.82	27	empty
4	179	0.57	0.81	27	empty
5	303	0.51	0.74	29	empty

Interfaces

7 interfaces between chains.

H–L · 1765 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1744 Å² buried · 15 hydrogen bonds · protein-protein
L–C · 898 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 662 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 652 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6UIG · Crystal structure of human monoclonal antibody H7.200 in complex with H7N9 hemagglutinin… · the same entry in another collection · chain G against G, 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
Every structure of UniProt A0A4Y5QYN9
Elsewhere: RCSB PDB 6UIG · PDBe 6UIG · UniProt A0A4Y5QYN9

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