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Crystal structure of a broadly neutralizing anti-HIV-1 antibody in complex with a peptide mimotope

Analyse Crystal structure of a broadly neutralizing anti-HIV-1 antibody in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1N0X
Type: protein
Length: 917 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin light chain; Immunoglobulin heavy chain; B2.1 peptide
UniProt: Q8TCD0, P0DOX5
Ligands: K, SO4
Pockets: 13 · best druggability 0.53

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Immunoglobulin light chain	protein	215	6% helix, 50% strand	Q8TCD0
H	Immunoglobulin heavy chain	protein	222	8% helix, 47% strand	P0DOX5
K	Immunoglobulin heavy chain	protein	224	8% helix, 47% strand	P0DOX5
P	B2.1 peptide	protein	21	0% helix, 38% strand	—
R	B2.1 peptide	protein	20	0% helix, 45% strand	—

Ligands and binding sites

K · Potassium ion · metal · chains P, R
SO4 · Sulfate ion · ion · 4 copies · chains H, K, P, R
GOL · Glycerol · additive · 8 copies · chains L, H, M, K
CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains H, R

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

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	309	0.53	0.74	38	empty
2	231	0.51	0.76	32	empty
3	264	0.50	0.74	37	empty
4	150	0.49	0.79	27	empty
5	184	0.49	0.76	31	GOL

Interfaces

12 interfaces between chains.

L–H · 1812 Å² buried · 16 hydrogen bonds · protein-protein
M–K · 1803 Å² buried · 12 hydrogen bonds · protein-protein
M–R · 398 Å² buried · 7 hydrogen bonds · protein-protein
L–P · 392 Å² buried · 7 hydrogen bonds · protein-protein
P–R · 330 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

1N0X · Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide… · 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 Q8TCD0
Every structure of UniProt P0DOX5
Elsewhere: RCSB PDB 1N0X · PDBe 1N0X · UniProt Q8TCD0 · UniProt P0DOX5

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