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Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide

Analyse Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HPY
Type: protein
Length: 443 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CH59 Fab heavy chain; CH59 Fab light chain; Envelope glycoprotein GP160
UniProt: Q9WLG7
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	CH59 Fab heavy chain	protein	219	10% helix, 50% strand	—
L	CH59 Fab light chain	protein	213	6% helix, 49% strand	—
P	Envelope glycoprotein GP160	protein	11	27% helix, 9% strand	Q9WLG7

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	689	0.65	0.74	80	empty
2	51	0.49	0.87	16	empty
3	102	0.42	0.78	24	GOL
4	110	0.39	0.75	24	empty

Interfaces

3 interfaces between chains.

H–L · 1715 Å² buried · 11 hydrogen bonds · protein-protein
L–P · 513 Å² buried · 8 hydrogen bonds · protein-protein
H–P · 434 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4HPY · Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide · 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 Q9WLG7
Elsewhere: RCSB PDB 4HPY · PDBe 4HPY · UniProt Q9WLG7

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