MolNFT v1 · #105355 · protein

Crystal structure of PGT124 Fab bound to HIV-1 jrcsf GP120 core and to CD4

4R2G · Surface protein GP160: “Crystal structure of PGT124 Fab bound to HIV-1 jrcsf GP120 core and to CD4”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #105355 on GenesisL1: 3D structure…

PDB: 4R2G
Type: protein
Length: 3,657 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Surface protein GP160; T-cell surface glycoprotein CD4; PGT124 light chain; PGT124 heavy…
UniProt: P20871, P01730, P0DOY3, P0DOX5
Ligands: NAG, MAN, BMA, CL
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 10 distinct chains · 8% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, O, K	Surface protein GP160	protein	303	17% helix, 34% strand	P20871
F, B	T-cell surface glycoprotein CD4	protein	175	5% helix, 49% strand	P01730
P, C, I, M	PGT124 light chain	protein	210	6% helix, 40% strand	P0DOY3
Q	PGT124 heavy chain	protein	228	7% helix, 53% strand	P0DOX5
D	PGT124 heavy chain	protein	225	3% helix, 50% strand	P0DOX5
H	T-cell surface glycoprotein CD4	protein	176	4% helix, 45% strand	P01730
J	PGT124 heavy chain	protein	226	5% helix, 51% strand	P0DOX5
L	T-cell surface glycoprotein CD4	protein	173	7% helix, 47% strand	P01730
N	PGT124 heavy chain	protein	228	4% helix, 54% strand	P0DOX5
A	Surface protein GP160	protein	302	17% helix, 35% strand	P20871

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains E, Q, D, O, N, A, J, K, F, L, H
MAN · alpha-D-mannopyranose · sugar · 28 copies · chains P, Q, C, D, M, N, A, I, J
BMA · beta-D-mannopyranose · sugar · 4 copies · chains Q, D, N, J
CL · Chloride ion · ion · 4 copies · chains E, O, A, K
GOL · Glycerol · additive · 4 copies

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	898	0.76	0.79	133	empty
2	74	0.73	0.98	22	empty
3	783	0.73	0.79	107	empty
4	62	0.73	0.98	18	empty
5	76	0.73	0.97	25	empty

Interfaces

32 interfaces between chains.

C–D · 2027 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1965 Å² buried · 13 hydrogen bonds · protein-protein
P–Q · 1930 Å² buried · 8 hydrogen bonds · protein-protein
M–N · 1911 Å² buried · 9 hydrogen bonds · protein-protein
B–O · 1060 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 46 disulfide, 32 glycan (disulfide, N-glycosylation).

Compared structures

4R2G · Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 · the same entry in another collection · chain K against K, 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 P20871
Every structure of UniProt P01730
Every structure of UniProt P0DOY3
Every structure of UniProt P0DOX5
Elsewhere: RCSB PDB 4R2G · PDBe 4R2G · UniProt P20871 · UniProt P01730 · UniProt P0DOY3 · UniProt P0DOX5

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