MolNFT v1 · #26763 · protein

Crystal structure of the fv fragment complexed with dansyl- lysine

1WZ1 · Ig light chain: “Crystal structure of the fv fragment complexed with dansyl- lysine”. X-ray diffraction, 1 ligand (DNS), 4 pockets (best druggability 0.56). MolNFT v1 #26763 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1WZ1
Type: protein
Length: 236 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig light chain; Ig heavy chain
Ligands: DNS
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Ig light chain	protein	113	3% helix, 50% strand	—
H	Ig heavy chain	protein	123	5% helix, 50% strand	—

Ligands and binding sites

DNS · N~6~-{[5-(dimethylamino)-1-naphthyl]sulfonyl}-L-lysine · ligand · chains L, H

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

Pockets

4 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	89	0.56	0.85	15	DNS
2	125	0.40	0.75	20	empty
3	110	0.39	0.75	24	empty
4	57	0.36	0.78	17	empty

Interfaces

1 interface between chains.

L–H · 796 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1WZ1 · Crystal structure of the Fv fragment complexed with dansyl-lysine · the same entry in another collection · chain L against L, 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 1WZ1 · PDBe 1WZ1

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