MolNFT v1 · #158321 · protein

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 env trimer in complex with 8ANC195 Fab

6NQD · T/F100 env GP120: “Cryo-EM structure of T/F100 SOSIP.664 HIV-1 env trimer in complex with 8ANC195 Fab”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.77). MolNFT v1 #158321 on GenesisL1: 3D…

PDB: 6NQD
Type: protein
Length: 2,403 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T/F100 env GP120; T/F100 env GP41; 8ANC195 G52K5 heavy chain, ig gamma-1 chain; 8ANC195…
UniProt: A0A140EMT3, S6B2A6, P0DOX7
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.77

Structure

electron microscopy · 4 distinct chains · 14% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	T/F100 env GP120	protein	439	10% helix, 35% strand	A0A140EMT3
B, F, J	T/F100 env GP41	protein	124	57% helix, 5% strand	A0A140EMT3
C, G, K	8ANC195 G52K5 heavy chain, ig gamma-1 chain	protein	130	0% helix, 45% strand	S6B2A6
D, H, L	8ANC195 G52K5 light chain	protein	108	3% helix, 46% strand	P0DOX7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 96 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
MAN · alpha-D-mannopyranose · sugar · 33 copies · chains C, D, G, H, K, L
BMA · beta-D-mannopyranose · sugar · 12 copies · chains C, D, G, H, K, L

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1117	0.77	0.79	149	empty
2	106	0.71	0.93	24	empty
3	688	0.68	0.76	78	empty
4	299	0.64	0.80	56	empty
5	332	0.63	0.79	51	empty

Interfaces

24 interfaces between chains.

A–B · 2234 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 2234 Å² buried · 8 hydrogen bonds · protein-protein
I–J · 2232 Å² buried · 8 hydrogen bonds · protein-protein
F–J · 1061 Å² buried · 7 hydrogen bonds · protein-protein
B–J · 1049 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 63 glycan, 39 disulfide (N-glycosylation, disulfide).

Compared structures

6NQD · Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab · the same entry in another collection · chain L against L, 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 A0A140EMT3
Every structure of UniProt S6B2A6
Every structure of UniProt P0DOX7
Elsewhere: RCSB PDB 6NQD · PDBe 6NQD · UniProt A0A140EMT3 · UniProt S6B2A6 · UniProt P0DOX7

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