MolNFT v1 · #167874 · protein

Crystal structure of nipah receptor binding protein head domain in complex with human neutralizing antibody henv-26

6VY5 · Anti-hendra receptor binding protein antibody henv-26 Fab…: “Crystal structure of nipah receptor binding protein head domain in complex with human neutralizing antibody…”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best…

PDB: 6VY5
Type: protein
Length: 835 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-hendra receptor binding protein antibody henv-26 Fab heavy chain; Anti-hendra…
UniProt: Q9IH62
Ligands: NAG
Pockets: 10 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-hendra receptor binding protein antibody henv-26 Fab heavy chain	protein	218	6% helix, 48% strand	—
L	Anti-hendra receptor binding protein antibody henv-26 Fab light chain	protein	208	8% helix, 50% strand	—
A	Receptor binding protein	protein	409	4% helix, 44% strand	Q9IH62

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, L

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

Pockets

10 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	697	0.71	0.78	57	empty
2	255	0.68	0.84	32	empty
3	142	0.62	0.85	40	empty
4	83	0.57	0.87	25	empty
5	145	0.54	0.81	26	empty

Interfaces

3 interfaces between chains.

H–L · 1607 Å² buried · 14 hydrogen bonds · protein-protein
H–A · 880 Å² buried · 8 hydrogen bonds · protein-protein
L–A · 457 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

6VY5 · Crystal structure of Nipah receptor binding protein head domain in complex with human… · 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
Every structure of UniProt Q9IH62
Elsewhere: RCSB PDB 6VY5 · PDBe 6VY5 · UniProt Q9IH62

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