MolNFT v1 · #74523 · protein

Crystal structure of anti-GP41 Fab nc-1

3OZ9 · Fab nc-1 kappa light chain: “Crystal structure of anti-GP41 Fab nc-1”. X-ray diffraction, 6 pockets (best druggability 0.56). MolNFT v1 #74523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OZ9
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab nc-1 kappa light chain; Fab nc-1 IGG2A heavy chain
UniProt: Q52L95, P01863
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab nc-1 kappa light chain	protein	211	6% helix, 54% strand	Q52L95
H	Fab nc-1 IGG2A heavy chain	protein	219	7% helix, 52% strand	P01863

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains L, H

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

Pockets

6 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	347	0.56	0.75	46	empty
2	96	0.44	0.79	22	empty
3	101	0.33	0.73	19	empty
4	77	0.31	0.74	17	empty
5	71	0.29	0.73	19	GOL

Interfaces

1 interface between chains.

L–H · 1800 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3OZ9 · Crystal Structure of anti-gp41 Fab NC-1 · the same entry in another collection · chain L against L, TM-score 1.00
P01863 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, a allele (P01863) · a predicted model of the same protein · chain H against A, TM-score 0.50

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q52L95
Every structure of UniProt P01863
Elsewhere: RCSB PDB 3OZ9 · PDBe 3OZ9 · UniProt Q52L95 · UniProt P01863

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