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Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab

Analyse Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DCQ
Type: protein
Length: 2,231 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP160; Immunoglobulin G PGT151 Fab, heavy chain; Immunoglobulin G…
UniProt: A0A2H4K974, S6B291, Q8TCD0
Ligands: NAG, MAN, BMA, FUC, GAL
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 15% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Envelope glycoprotein GP160	protein	435	11% helix, 35% strand	A0A2H4K974
B	Envelope glycoprotein GP160	protein	122	44% helix, 7% strand	A0A2H4K974
C	Envelope glycoprotein GP160	protein	452	10% helix, 38% strand	A0A2H4K974
D	Envelope glycoprotein GP160	protein	146	47% helix, 5% strand	A0A2H4K974
E	Envelope glycoprotein GP160	protein	448	11% helix, 37% strand	A0A2H4K974
F	Envelope glycoprotein GP160	protein	139	43% helix, 9% strand	A0A2H4K974
H	Immunoglobulin G PGT151 Fab, heavy chain	protein	132	2% helix, 19% strand	S6B291
L	Immunoglobulin G PGT151 Fab, light chain	protein	110	0% helix, 33% strand	Q8TCD0
M	Immunoglobulin G PGT151 Fab, heavy chain	protein	135	0% helix, 48% strand	S6B291
N	Immunoglobulin G PGT151 Fab, light chain	protein	112	0% helix, 45% strand	Q8TCD0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 100 copies · chains A, C, B, E, D, M, F, N, H, L
MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, C, M, N, E, H, L
BMA · beta-D-mannopyranose · sugar · 7 copies · chains M, H
FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, C, D, M, E, F, H
GAL · beta-D-galactopyranose · sugar · 4 copies · chains F, M, B, H

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1018	0.81	0.82	87	empty
2	887	0.79	0.82	85	empty
3	1034	0.78	0.80	111	empty
4	560	0.77	0.83	69	NAG
5	290	0.74	0.87	50	NAG

Interfaces

24 interfaces between chains.

C–D · 3169 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2898 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2266 Å² buried · 20 hydrogen bonds · protein-protein
D–F · 1148 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 1134 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 59 glycan, 34 disulfide (N-glycosylation, disulfide, glycosylation).

Compared structures

6DCQ · Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with… · 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 A0A2H4K974
Every structure of UniProt S6B291
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 6DCQ · PDBe 6DCQ · UniProt A0A2H4K974 · UniProt S6B291 · UniProt Q8TCD0

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