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The structure of the unbound form of anti-HIV antibody 4E10 fv

Analyse The structure of the unbound form of anti-HIV antibody 4E10 fv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LLV
Type: protein
Length: 895 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4E10 fv heavy chain; 4E10 fv light chain
Ligands: SO4
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	4E10 fv heavy chain	protein	127	8% helix, 50% strand	—
B	4E10 fv light chain	protein	111	5% helix, 45% strand	—
D	4E10 fv light chain	protein	74	4% helix, 49% strand	—
E	4E10 fv heavy chain	protein	121	8% helix, 48% strand	—
F	4E10 fv light chain	protein	102	6% helix, 43% strand	—
H	4E10 fv heavy chain	protein	125	5% helix, 46% strand	—
L	4E10 fv light chain	protein	108	6% helix, 49% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, F, L, C, H, B
GOL · Glycerol · additive · 6 copies · chains A, E, H, B, C, F, L

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	541	0.76	0.83	72	SO4
2	709	0.72	0.78	65	SO4, GOL
3	251	0.56	0.78	25	empty
4	272	0.54	0.76	53	empty
5	191	0.53	0.78	24	empty

Interfaces

19 interfaces between chains.

E–F · 745 Å² buried · 8 hydrogen bonds · protein-protein
H–L · 716 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 664 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 595 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 535 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4LLV · The structure of the unbound form of anti-HIV antibody 4E10 Fv · the same entry in another collection · chain A against A, 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 4LLV · PDBe 4LLV

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