MolNFT v1 · #119838 · protein

Pd-L1 in complex with bms-936559 Fab

5GGT · Programmed cell death 1 ligand 1: “Pd-L1 in complex with bms-936559 Fab”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #119838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GGT
Type: protein
Length: 542 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death 1 ligand 1; IgG H chain; Igk@ protein
UniProt: Q9NZQ7
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death 1 ligand 1	protein	116	10% helix, 43% strand	Q9NZQ7
H	IgG H chain	protein	216	3% helix, 47% strand	—
L	Igk@ protein	protein	210	6% helix, 47% 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	258	0.54	0.76	32	empty
2	204	0.46	0.74	34	empty
3	68	0.38	0.78	21	empty

Interfaces

3 interfaces between chains.

H–L · 1731 Å² buried · 22 hydrogen bonds · protein-protein
A–H · 587 Å² buried · 3 hydrogen bonds · protein-protein
A–L · 218 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5GGT · PD-L1 in complex with BMS-936559 Fab · 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 5GGT · PDBe 5GGT · UniProt Q9NZQ7

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