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Crystal structure of the BG505 sosip GP140 HIV-1 env trimer in complex with the broadly neutralizing Fab PGT122 and scfv NIH45-46

Analyse Crystal structure of the BG505 sosip GP140 HIV-1 env trimer in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D9Q
Type: protein
Length: 3,678 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP120; Envelope glycoprotein GP41; PGT122 light CHAIN,IG lambda-3…
UniProt: Q2N0S6, Q2N0S9, P0CG06, S6B291
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 13% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, A, J	Envelope glycoprotein GP120	protein	448	14% helix, 39% strand	Q2N0S6
B, C, K	Envelope glycoprotein GP41	protein	121	52% helix, 6% strand	Q2N0S9
L, E, M	PGT122 light CHAIN,IG lambda-3 chain C regions	protein	208	5% helix, 46% strand	P0CG06
H, F, N	PGT122 heavy CHAIN,IGG H chain	protein	227	5% helix, 52% strand	S6B291
D, I, O	NIH45-46 single chain fv	protein	222	4% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 102 copies · chains G, B, L, H, J, D, A, C, E, F, I, K, M, N, O
MAN · alpha-D-mannopyranose · sugar · 90 copies · chains H, G, D, I, L, F, A, O, E, N, J, M
BMA · beta-D-mannopyranose · sugar · 24 copies · chains H, D, F, I, N, O

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	162	0.76	0.93	24	empty
2	149	0.74	0.92	37	NAG
3	231	0.70	0.86	51	NAG
4	237	0.70	0.85	55	NAG
5	623	0.69	0.78	63	empty

Interfaces

27 interfaces between chains.

G–B · 2656 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 2611 Å² buried · 17 hydrogen bonds · protein-protein
J–K · 2605 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 2027 Å² buried · 14 hydrogen bonds · protein-protein
M–N · 2018 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 60 glycan, 54 disulfide, 3 modified (N-glycosylation, disulfide, cyclization).

Compared structures

5D9Q · Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly… · the same entry in another collection · chain G against G, 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
Every structure of UniProt Q2N0S9
Every structure of UniProt P0CG06
Every structure of UniProt S6B291
Elsewhere: RCSB PDB 5D9Q · PDBe 5D9Q · UniProt Q2N0S6 · UniProt Q2N0S9 · UniProt P0CG06 · UniProt S6B291

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