MolNFT v1 · #159718 · protein

Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 clade A/E strain 93TH057 GP120 core.

6OZ2 · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 clade A/E strain…”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.77). MolNFT v1 #159718…

PDB: 6OZ2
Type: protein
Length: 763 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clade A/E 93TH057 HIV-1 GP120 core; N49P6 antibody Fab heavy chain; N49P6 antibody Fab…
UniProt: A0A0M3KKW9
Ligands: NAG
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Clade A/E 93TH057 HIV-1 GP120 core	protein	338	18% helix, 36% strand	A0A0M3KKW9
H	N49P6 antibody Fab heavy chain	protein	225	4% helix, 52% strand	—
L	N49P6 antibody Fab light chain	protein	200	6% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.77	0.94	34	empty
2	402	0.74	0.84	48	empty
3	609	0.67	0.76	58	empty
4	52	0.62	0.93	16	empty
5	209	0.51	0.77	46	empty

Interfaces

3 interfaces between chains.

H–L · 1725 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 826 Å² buried · 12 hydrogen bonds · protein-protein
G–L · 179 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 11 glycan (disulfide, N-glycosylation).

Compared structures

6OZ2 · Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1… · 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 A0A0M3KKW9
Elsewhere: RCSB PDB 6OZ2 · PDBe 6OZ2 · UniProt A0A0M3KKW9

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