Research workbench

Crystal structure of HIV epitope-scaffold 4E10 fv complex

Analyse Crystal structure of HIV epitope-scaffold 4E10 fv complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H3P
Type: protein
Length: 510 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fv 4E10 heavy chain; Fv 4E10 light chain; 4E10_S0_1TJLC_004_N
Ligands: CA
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 6 distinct chains · 10% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fv 4E10 heavy chain	protein	125	5% helix, 54% strand	—
I	Fv 4E10 heavy chain	protein	126	5% helix, 56% strand	—
L	Fv 4E10 light chain	protein	109	6% helix, 48% strand	—
M	Fv 4E10 light chain	protein	111	5% helix, 44% strand	—
S	4E10_S0_1TJLC_004_N	protein	18	67% helix, 0% strand	—
T	4E10_S0_1TJLC_004_N	protein	21	81% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · chains H, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	275	0.54	0.76	33	empty
2	143	0.46	0.77	26	empty
3	117	0.37	0.74	27	empty
4	69	0.36	0.77	18	empty
5	51	0.27	0.74	16	empty

Interfaces

8 interfaces between chains.

H–L · 765 Å² buried · 8 hydrogen bonds · protein-protein
I–M · 730 Å² buried · 5 hydrogen bonds · protein-protein
I–T · 570 Å² buried · 5 hydrogen bonds · protein-protein
H–I · 556 Å² buried · 4 hydrogen bonds · protein-protein
H–S · 533 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3H3P · Crystal structure of HIV epitope-scaffold 4E10 Fv complex · 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 3H3P · PDBe 3H3P

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.