Research workbench

Triple helix bundle of GP41 complexed with Fab 8066

Analyse Triple helix bundle of GP41 complexed with Fab 8066 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KHT
Type: protein
Length: 489 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GP41 helix; 8066 heavy chain; 8066 light chain
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GP41 helix	protein	66	65% helix, 0% strand	—
H	8066 heavy chain	protein	214	7% helix, 49% strand	—
L	8066 light chain	protein	209	2% helix, 38% strand	—

Pockets

3 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	345	0.51	0.73	49	empty
2	159	0.48	0.77	37	empty
3	59	0.29	0.74	15	empty

Interfaces

3 interfaces between chains.

H–L · 1602 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 663 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 205 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4KHT · Triple helix bundle of GP41 complexed with fab 8066 · 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 4KHT · PDBe 4KHT

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