MolNFT v1 · #121883 · protein

Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer in complex with V3 loop-targeting antibody PGT122 Fab and fusion peptide-targeting antibody VRC34.01 Fab

5I8H · BG505 SOSIP.664 GP120: “Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer in complex with V3 loop-targeting antibody…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.72). MolNFT v1…

PDB: 5I8H
Type: protein
Length: 2,915 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BG505 SOSIP.664 GP120; BG505 SOSIP.664 GP41; PGT122 Fab light chain; VRC34.01 Fab heavy…
UniProt: Q2N0S6
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 7 distinct chains · 12% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BG505 SOSIP.664 GP120	protein	455	11% helix, 36% strand	Q2N0S6
B, D	BG505 SOSIP.664 GP41	protein	132	52% helix, 7% strand	Q2N0S6
C	BG505 SOSIP.664 GP120	protein	450	12% helix, 37% strand	Q2N0S6
L, J	PGT122 Fab light chain	protein	210	5% helix, 47% strand	—
E, G	VRC34.01 Fab heavy chain	protein	223	9% helix, 50% strand	—
F, H	VRC34.01 Fab light chain	protein	212	6% helix, 50% strand	—
I, K	PGT122 Fab heavy chain	protein	228	5% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 70 copies · chains A, B, E, F, J, I, C, G, D, H, L, K
MAN · alpha-D-mannopyranose · sugar · 33 copies · chains F, A, I, J, H, C, L, K
BMA · beta-D-mannopyranose · sugar · 13 copies · chains F, K, I, 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1168	0.72	0.76	105	empty
2	73	0.71	0.96	27	empty
3	425	0.70	0.81	64	NAG
4	60	0.67	0.95	26	empty
5	261	0.66	0.82	49	NAG

Interfaces

22 interfaces between chains.

C–D · 2582 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 2566 Å² buried · 18 hydrogen bonds · protein-protein
I–J · 2049 Å² buried · 15 hydrogen bonds · protein-protein
L–K · 2028 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1863 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 glycan, 38 disulfide (N-glycosylation, disulfide, glycosylation).

Compared structures

5I8H · Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3… · 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 Q2N0S6
Elsewhere: RCSB PDB 5I8H · PDBe 5I8H · UniProt Q2N0S6

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