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Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade C strain ZM176.66 GP120

Analyse Crystal structure of broadly and potently neutralizing antibody VRC01 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LST
Type: protein
Length: 771 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP120 of HIV-1 clade C; Heavy chain of antibody VRC01; Light chain…
UniProt: R4GRV3
Ligands: NAG
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Envelope glycoprotein GP120 of HIV-1 clade C	protein	339	17% helix, 36% strand	R4GRV3
H	Heavy chain of antibody VRC01	protein	222	7% helix, 48% strand	—
L	Light chain of antibody VRC01	protein	210	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains G, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	347	0.75	0.86	42	empty
2	154	0.74	0.92	33	empty
3	202	0.68	0.86	24	empty
4	296	0.64	0.81	43	empty
5	60	0.50	0.86	20	empty

Interfaces

3 interfaces between chains.

H–L · 1919 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 1039 Å² buried · 17 hydrogen bonds · protein-protein
G–L · 356 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

4LST · Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with… · the same entry in another collection · chain L against L, 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 R4GRV3
Elsewhere: RCSB PDB 4LST · PDBe 4LST · UniProt R4GRV3

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