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Crystal structure of the anti-HIV-1 antibody 2.2C

Analyse Crystal structure of the anti-HIV-1 antibody 2.2C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R4B
Type: protein
Length: 1,708 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 2.2C light chain; Fab 2.2C heavy chain
Ligands: NAG, SO4
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Fab 2.2C light chain	protein	210	7% helix, 50% strand	—
H, B, D, F	Fab 2.2C heavy chain	protein	220	8% helix, 51% strand	—
C, E	Fab 2.2C light chain	protein	204	6% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, B, D, F
SO4 · Sulfate ion · ion · 36 copies · chains L, H, D, F, A, B, C, E

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1026	0.70	0.74	60	SO4
2	875	0.68	0.74	90	SO4
3	813	0.67	0.74	90	SO4
4	366	0.57	0.75	47	empty
5	50	0.53	0.90	20	empty

Interfaces

14 interfaces between chains.

C–D · 2000 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1979 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1943 Å² buried · 17 hydrogen bonds · protein-protein
L–H · 1940 Å² buried · 15 hydrogen bonds · protein-protein
H–D · 704 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4R4B · Crystal structure of the anti-hiv-1 antibody 2.2c · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 4R4B · PDBe 4R4B

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