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Crystal structure BG505 sosip GP140 HIV-1 env trimer bound to broadly neutralizing antibodies PGT128 and 8ANC195

Analyse Crystal structure BG505 sosip GP140 HIV-1 env trimer bound to broadly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C7K
Type: protein
Length: 1,442 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody Fab PGT128 heavy chain; Antibody Fab PGT128 light chain; Envelope glycoprotein…
UniProt: S6B291, C6KXN3, Q2N0S6, P01857, P01834
Ligands: MAN, NAG, BMA, SO4
Pockets: 17 · best druggability 0.71

Structure

x-ray diffraction · 6 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody Fab PGT128 heavy chain	protein	230	1% helix, 54% strand	S6B291
B	Antibody Fab PGT128 light chain	protein	204	6% helix, 49% strand	C6KXN3
C	Envelope glycoprotein GP120	protein	450	12% helix, 37% strand	Q2N0S6
D	Envelope glycoprotein GP41	protein	122	44% helix, 6% strand	Q2N0S6
E	Antibody Fab 8ANC195 heavy chain	protein	224	3% helix, 51% strand	P01857
F	Antibody Fab 8ANC195 light chain	protein	212	6% helix, 49% strand	P01834

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 38 copies · chains E, F, A, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, C, E, D, F
BMA · beta-D-mannopyranose · sugar · 10 copies · chains E, A, B, C, F
SO4 · Sulfate ion · ion · chains C

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.71	0.96	21	empty
2	575	0.67	0.77	57	empty
3	221	0.65	0.84	24	empty
4	262	0.65	0.82	49	NAG
5	228	0.64	0.83	32	empty

Interfaces

7 interfaces between chains.

C–D · 2458 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 2001 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1818 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 855 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 601 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 glycan, 21 disulfide (disulfide, N-glycosylation, glycosylation).

Compared structures

5C7K · Crystal structure BG505 SOSIP gp140 HIV-1 Env trimer bound to broadly neutralizing… · the same entry in another collection · chain C against C, TM-score 1.00
P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain F against A, TM-score 0.48

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 S6B291
Every structure of UniProt C6KXN3
Every structure of UniProt Q2N0S6
Every structure of UniProt P01857
Every structure of UniProt P01834
Elsewhere: RCSB PDB 5C7K · PDBe 5C7K · UniProt S6B291 · UniProt C6KXN3 · UniProt Q2N0S6 · UniProt P01857 · UniProt P01834

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