MolNFT v1 · #100951 · protein

Crystal structure of the BG505 sosip GP140 HIV-1 env trimer in complex with the broadly neutralizing Fab PGT122

4NCO · BG505 sosip GP120: “Crystal structure of the BG505 sosip GP140 HIV-1 env trimer in complex with the broadly neutralizing Fab…”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 20 pockets (best druggability 0.81). MolNFT v1 #100951 on…

PDB: 4NCO
Type: protein
Length: 2,775 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BG505 sosip GP120; BG505 sosip GP41; PGT122 light chain; PGT122 heavy chain
UniProt: Q2N0S6
Ligands: MAN, NAG, BMA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	BG505 sosip GP120	protein	420	14% helix, 31% strand	Q2N0S6
B, F, J	BG505 sosip GP41	protein	77	92% helix, 0% strand	—
C, G, K	PGT122 light chain	protein	202	7% helix, 47% strand	—
D, H, L	PGT122 heavy chain	protein	226	9% helix, 52% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 72 copies · chains D, A, C, H, E, G, L, I, K
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, D, C, E, H, G, I, L, K
BMA · beta-D-mannopyranose · sugar · 15 copies · chains D, H, L

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.81	0.82	112	empty
2	1137	0.77	0.79	136	empty
3	449	0.75	0.84	68	empty
4	428	0.74	0.84	60	empty
5	448	0.73	0.82	65	empty

Interfaces

21 interfaces between chains.

C–D · 1889 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1886 Å² buried · 15 hydrogen bonds · protein-protein
K–L · 1884 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 291 Å² buried · 0 hydrogen bonds · protein-protein
I–K · 261 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 45 glycan, 39 disulfide (N-glycosylation, disulfide).

Compared structures

4NCO · Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly… · 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 4NCO · PDBe 4NCO · UniProt Q2N0S6

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