MolNFT v1 · #143880 · protein

Crystal structure of broadly neutralizing antibody N49P7 in complex with HIV-1 clade ae strain 93TH057 GP120 core.

6BCK · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of broadly neutralizing antibody N49P7 in complex with HIV-1 clade ae strain 93TH057 GP120…”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.69). MolNFT v1…

PDB: 6BCK
Type: protein
Length: 758 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clade A/E 93TH057 HIV-1 GP120 core; N49P7 Fab heavy chain of N29P7 IgG; N49P7 Fab light…
UniProt: A0A0M3KKW9
Ligands: NAG
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Clade A/E 93TH057 HIV-1 GP120 core	protein	337	18% helix, 34% strand	A0A0M3KKW9
H	N49P7 Fab heavy chain of N29P7 IgG	protein	222	4% helix, 46% strand	—
L	N49P7 Fab light chain from N49P7 IgG	protein	199	5% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, H, L
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains G, H, L

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

Pockets

8 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	213	0.69	0.86	41	empty
2	583	0.66	0.76	77	empty
3	219	0.53	0.77	31	MPD
4	69	0.53	0.86	18	NAG
5	199	0.53	0.78	38	empty

Interfaces

3 interfaces between chains.

H–L · 1762 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 935 Å² buried · 19 hydrogen bonds · protein-protein
G–L · 176 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

6BCK · Crystal Structure of Broadly Neutralizing Antibody N49P7 in Complex with HIV-1 Clade AE… · 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 6BCK · PDBe 6BCK · UniProt A0A0M3KKW9

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