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Crystal structure of antibody VRC07 in complex with clade A/E 93TH057 HIV-1 GP120 core

Analyse Crystal structure of antibody VRC07 in complex with clade A/E 93TH057 HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OLU
Type: protein
Length: 778 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP160; Antigen binding fragment of heavy chain: antibody VRC01…
UniProt: Q0ED31
Ligands: NAG
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Envelope glycoprotein GP160	protein	342	18% helix, 37% strand	Q0ED31
H	Antigen binding fragment of heavy chain: antibody VRC01	protein	228	8% helix, 52% strand	—
L	Antigen binding fragment of light chain: antibody VRC01	protein	208	5% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, H, L

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	476	0.80	0.88	75	empty
2	259	0.58	0.78	29	empty
3	81	0.53	0.85	18	NAG
4	117	0.40	0.76	19	empty
5	67	0.34	0.76	20	empty

Interfaces

3 interfaces between chains.

H–L · 1870 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1036 Å² buried · 17 hydrogen bonds · protein-protein
G–L · 231 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

4OLU · Crystal structure of antibody VRC07 in complex with clade A/E 93TH057 HIV-1 gp120 core · 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 Q0ED31
Elsewhere: RCSB PDB 4OLU · PDBe 4OLU · UniProt Q0ED31

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