MolNFT v1 · #70342 · protein

Crystal structure of HIV epitope-scaffold 4E10_D0_1ISEA_004_N 4E10 fv complex

3LHP · Fv 4E10 heavy chain: “Crystal structure of HIV epitope-scaffold 4E10_D0_1ISEA_004_N 4E10 fv complex”. X-ray diffraction, 5 pockets (best druggability 0.80). MolNFT v1 #70342 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3LHP
Type: protein
Length: 693 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_D0_1ISEA_004_N (T93)
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fv 4E10 heavy chain	protein	124	5% helix, 54% strand	—
I	Fv 4E10 heavy chain	protein	122	5% helix, 50% strand	—
L	Fv 4E10 light chain	protein	111	5% helix, 46% strand	—
M	Fv 4E10 light chain	protein	110	5% helix, 48% strand	—
S	4E10_D0_1ISEA_004_N (T93)	protein	116	88% helix, 0% strand	—
T	4E10_D0_1ISEA_004_N (T93)	protein	110	85% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains M

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	1120	0.80	0.81	82	empty
2	115	0.39	0.75	25	empty
3	64	0.33	0.76	16	empty
4	75	0.29	0.73	20	empty
5	61	0.28	0.74	17	empty

Interfaces

10 interfaces between chains.

I–M · 741 Å² buried · 9 hydrogen bonds · protein-protein
H–L · 710 Å² buried · 7 hydrogen bonds · protein-protein
H–S · 709 Å² buried · 2 hydrogen bonds · protein-protein
I–T · 632 Å² buried · 2 hydrogen bonds · protein-protein
L–M · 323 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3LHP · Crystal structure of HIV epitope-scaffold 4E10_D0_1ISEA_004_N 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 3LHP · PDBe 3LHP

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