MolNFT v1 · #115442 · protein

Crystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 HIV-1 env trimer

5CJX · 8ANC195 G52K5 heavy chain, ig gamma-1 chain: “Crystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 HIV-1 env trimer”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.80). MolNFT v1 #115442…

PDB: 5CJX
Type: protein
Length: 2,886 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 8ANC195 G52K5 heavy chain, ig gamma-1 chain; BG505 env GP41; 8ANC195 G52K5 light chain…
UniProt: Q2N0S6
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 9 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	8ANC195 G52K5 heavy chain, ig gamma-1 chain	protein	224	4% helix, 52% strand	—
B	BG505 env GP41	protein	124	62% helix, 6% strand	Q2N0S6
C, E, L	8ANC195 G52K5 light chain	protein	214	5% helix, 51% strand	—
G	BG505 env GP120	protein	398	16% helix, 36% strand	Q2N0S6
H	8ANC195 G52K5 heavy chain, ig gamma-1 chain	protein	227	4% helix, 51% strand	—
J	BG505 env GP41	protein	124	61% helix, 6% strand	Q2N0S6
K	BG505 env GP120	protein	405	16% helix, 37% strand	Q2N0S6
X	BG505 env GP41	protein	121	64% helix, 6% strand	Q2N0S6
Y	BG505 env GP120	protein	397	15% helix, 35% strand	Q2N0S6

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains B, H, L, G, J, C, A, K, X, E, D, Y
MAN · alpha-D-mannopyranose · sugar · 33 copies · chains L, H, C, A, D
BMA · beta-D-mannopyranose · sugar · 11 copies · chains L, H, C, A, E, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.80	0.81	94	empty
2	536	0.78	0.84	59	NAG
3	597	0.77	0.82	57	NAG
4	273	0.74	0.87	52	empty
5	346	0.72	0.84	41	NAG

Interfaces

24 interfaces between chains.

J–K · 2662 Å² buried · 16 hydrogen bonds · protein-protein
X–Y · 2498 Å² buried · 17 hydrogen bonds · protein-protein
B–G · 2483 Å² buried · 19 hydrogen bonds · protein-protein
H–L · 1849 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1831 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 41 disulfide, 23 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

5CJX · Crystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 HIV-1 Env trimer · the same entry in another collection · chain A against A, 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 Q2N0S6
Elsewhere: RCSB PDB 5CJX · PDBe 5CJX · UniProt Q2N0S6

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