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Crystal structure of PG9 Fab in complex with V1V2 region from HIV-1 strain ZM109

Analyse Crystal structure of PG9 Fab in complex with V1V2 region from HIV-1 strain ZM109 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U2S
Type: protein
Length: 1,059 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PG9 heavy chain; PG9 light chain; Envelope glycoprotein GP120
Ligands: MAN, NAG, BMA, SO4
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	PG9 heavy chain	protein	230	9% helix, 56% strand	—
L, B	PG9 light chain	protein	211	8% helix, 51% strand	—
G	Envelope glycoprotein GP120	protein	90	17% helix, 58% strand	—
A	PG9 heavy chain	protein	227	9% helix, 55% strand	—
C	Envelope glycoprotein GP120	protein	90	16% helix, 59% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 8 copies · chains H, L, G, A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains H, G, A, C
BMA · beta-D-mannopyranose · sugar · 2 copies
SO4 · Sulfate ion · ion · 5 copies · chains H, L, A, B
BU3 · (R,R)-2,3-butanediol · additive · 2 copies · chains H, L, A, B

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1069	0.75	0.78	104	empty
2	239	0.54	0.77	31	BU3
3	235	0.51	0.75	26	empty
4	119	0.51	0.81	24	empty
5	109	0.43	0.77	22	MAN

Interfaces

9 interfaces between chains.

H–L · 1727 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1724 Å² buried · 15 hydrogen bonds · protein-protein
H–G · 645 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 595 Å² buried · 13 hydrogen bonds · protein-protein
L–A · 327 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 6 modified, 4 glycan (disulfide, N-glycosylation, sulfation, cyclization).

Compared structures

3U2S · Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109 · 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
Elsewhere: RCSB PDB 3U2S · PDBe 3U2S

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