Research workbench

Pd-L1 igv domain V76T with fragment

Analyse Pd-L1 igv domain V76T with fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NOJ
Type: protein
Length: 251 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death 1 ligand 1
UniProt: Q9NZQ7
Ligands: KW7
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death 1 ligand 1	protein	125	17% helix, 42% strand	Q9NZQ7
B	Programmed cell death 1 ligand 1	protein	126	17% helix, 41% strand	Q9NZQ7

Ligands and binding sites

KW7 · methyl 3-amino-4-(2-fluorophenyl)-1H-pyrrole-2-carboxylate · ligand · chains A, B

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	107	0.65	0.89	23	KW7
2	53	0.31	0.77	15	empty
3	65	0.31	0.75	11	empty
4	54	0.29	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 570 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6NOJ · PD-L1 IgV domain V76T with fragment · 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
Every structure of UniProt Q9NZQ7
Elsewhere: RCSB PDB 6NOJ · PDBe 6NOJ · UniProt Q9NZQ7

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