Research workbench

BG505 SOSIP.664 in complex with broadly neutralizing antibodies PG9 and 8ANC195

Analyse BG505 SOSIP.664 in complex with broadly neutralizing antibodies PG9 and 8ANC195 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VJ6
Type: protein
Length: 3,479 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP160; PG9 Fab heavy chain; 8ANC195 Fab heavy chain; 8ANC195 Fab…
UniProt: Q2N0S6, P0DOX5, S6B291, Q8TCD0, Q6GMW3
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 6 distinct chains · 10% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Envelope glycoprotein GP160	protein	126	44% helix, 2% strand	Q2N0S6
D, E, F	Envelope glycoprotein GP160	protein	449	12% helix, 35% strand	Q2N0S6
H	PG9 Fab heavy chain	protein	229	3% helix, 44% strand	P0DOX5
M, O, Q	8ANC195 Fab heavy chain	protein	224	4% helix, 51% strand	S6B291
N, P, R	8ANC195 Fab light chain	protein	214	4% helix, 51% strand	Q8TCD0
L	PG9 Fab light chain	protein	211	6% helix, 50% strand	Q6GMW3

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.81	0.88	63	empty
2	563	0.80	0.86	88	empty
3	583	0.78	0.84	78	empty
4	701	0.76	0.82	75	empty
5	1093	0.71	0.75	65	empty

Interfaces

28 interfaces between chains.

A–D · 2670 Å² buried · 34 hydrogen bonds · protein-protein
B–E · 2665 Å² buried · 32 hydrogen bonds · protein-protein
C–F · 2649 Å² buried · 33 hydrogen bonds · protein-protein
Q–R · 1734 Å² buried · 12 hydrogen bonds · protein-protein
O–P · 1732 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 49 disulfide, 2 modified (disulfide, sulfation).

Compared structures

5VJ6 · BG505 SOSIP.664 in complex with broadly neutralizing antibodies PG9 and 8ANC195 · the same entry in another collection · chain E against E, 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
Every structure of UniProt P0DOX5
Every structure of UniProt S6B291
Every structure of UniProt Q8TCD0
Every structure of UniProt Q6GMW3
Elsewhere: RCSB PDB 5VJ6 · PDBe 5VJ6 · UniProt Q2N0S6 · UniProt P0DOX5 · UniProt S6B291 · UniProt Q8TCD0 · UniProt Q6GMW3

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