MolNFT v1 · #179696 · protein

BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human GP120-GP41 interface antibody 8ANC195

7KDE · HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41: “BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human GP120-GP41 interface…”. Electron microscopy, 4 ligands (NAG, MAN, BMA), 20 pockets (best…

PDB: 7KDE
Type: protein
Length: 3,069 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41; Envelope glycoprotein GP120; Ab 1485…
UniProt: Q2N0S6
Ligands: NAG, MAN, BMA, FUC
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 6 distinct chains · 10% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41	protein	123	49% helix, 6% strand	Q2N0S6
E, F, G	Envelope glycoprotein GP120	protein	429	7% helix, 34% strand	Q2N0S6
H, J, M	Ab 1485 heavy chain	protein	129	0% helix, 29% strand	—
O, Q, S	8ANC195 Fab heavy chain	protein	132	2% helix, 48% strand	—
P, R, T	8ANC195 Fab light chain	protein	107	3% helix, 31% strand	—
I, L, N	Ab 1485 light chain	protein	103	3% helix, 32% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, T, S, B, P, O, C, R, Q, E, M, F, J, G, H
MAN · alpha-D-mannopyranose · sugar · 35 copies · chains M, S, N, Q, J, I, H, O, L
BMA · beta-D-mannopyranose · sugar · 15 copies · chains T, R, M, S, J, Q, H, O
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B

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	477	0.83	0.90	56	empty
2	374	0.69	0.82	58	NAG
3	78	0.69	0.95	27	empty
4	296	0.69	0.83	46	NAG
5	61	0.68	0.96	20	empty

Interfaces

30 interfaces between chains.

B–G · 2579 Å² buried · 20 hydrogen bonds · protein-protein
C–F · 2563 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 2556 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1018 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 998 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 58 glycan, 45 disulfide (N-glycosylation, disulfide).

Compared structures

7KDE · BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human… · the same entry in another collection · chain H against H, 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 7KDE · PDBe 7KDE · UniProt Q2N0S6

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