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HIV-1 bnab 1-55 in complex with modified BG505 sosip-based immunogen RC1 and 10-1074

Analyse HIV-1 bnab 1-55 in complex with modified BG505 sosip-based immunogen RC1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UDK
Type: protein
Length: 3,129 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RC1 variant of HIV-1 env glycoprotein GP120; 10-1074 Fab heavy chain; 10-1074 Fab light…
UniProt: S6B2B6, Q8N355, S6C4S0, Q6PJF2
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 6 distinct chains · 10% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, K, R	RC1 variant of HIV-1 env glycoprotein GP120	protein	442	9% helix, 34% strand	—
A, F, O	10-1074 Fab heavy chain	protein	133	0% helix, 44% strand	S6B2B6
B, I, P	10-1074 Fab light chain	protein	107	0% helix, 27% strand	Q8N355
M, D, H	1-55 Fab heavy chain	protein	130	0% helix, 33% strand	S6C4S0
N, E, L	1-55 Fab light chain	protein	108	3% helix, 43% strand	Q6PJF2
C, J, Q	RC1 variant of HIV-1 env glycoprotein GP41	protein	123	47% helix, 6% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains G, D, E, A, K, H, L, F, R, M, O, N, C, J, Q
MAN · alpha-D-mannopyranose · sugar · 23 copies · chains G, A, B, K, F, I, R, D, O, P
BMA · beta-D-mannopyranose · sugar · 8 copies · chains E, A, L, F, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.81	0.95	42	empty
2	754	0.74	0.79	77	empty
3	546	0.72	0.81	72	empty
4	752	0.70	0.77	53	empty
5	442	0.69	0.81	64	empty

Interfaces

33 interfaces between chains.

G–C · 2661 Å² buried · 12 hydrogen bonds · protein-protein
K–J · 2626 Å² buried · 13 hydrogen bonds · protein-protein
R–Q · 2620 Å² buried · 15 hydrogen bonds · protein-protein
G–D · 1269 Å² buried · 13 hydrogen bonds · protein-protein
K–H · 1206 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 glycan, 39 disulfide (N-glycosylation, disulfide).

Compared structures

6UDK · HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074 · 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 S6B2B6
Every structure of UniProt Q8N355
Every structure of UniProt S6C4S0
Every structure of UniProt Q6PJF2
Elsewhere: RCSB PDB 6UDK · PDBe 6UDK · UniProt S6B2B6 · UniProt Q8N355 · UniProt S6C4S0 · UniProt Q6PJF2

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