MolNFT v1 · #139210 · protein

Pd-L1 in complex with atezolizumab

5X8L · Programmed cell death 1 ligand 1: “Pd-L1 in complex with atezolizumab”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #139210 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X8L
Type: protein
Length: 2,674 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death 1 ligand 1; Atezolizumab light chain; Atezolizumab heavy chain
UniProt: Q9NZQ7
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 11 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death 1 ligand 1	protein	113	11% helix, 49% strand	Q9NZQ7
K, M, O	Atezolizumab light chain	protein	213	6% helix, 49% strand	—
F	Atezolizumab heavy chain	protein	212	6% helix, 53% strand	—
B, C, D	Programmed cell death 1 ligand 1	protein	116	13% helix, 44% strand	Q9NZQ7
L	Atezolizumab light chain	protein	202	4% helix, 45% strand	—
G	Atezolizumab heavy chain	protein	211	9% helix, 54% strand	—
H	Atezolizumab heavy chain	protein	212	3% helix, 53% strand	—
N	Atezolizumab light chain	protein	204	4% helix, 45% strand	—
S	Atezolizumab heavy chain	protein	211	6% helix, 51% strand	—
E	Programmed cell death 1 ligand 1	protein	114	5% helix, 49% strand	Q9NZQ7
J	Atezolizumab heavy chain	protein	208	6% helix, 54% strand	—

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1196	0.81	0.83	125	empty
2	1058	0.81	0.82	119	empty
3	1105	0.80	0.82	110	empty
4	842	0.74	0.78	74	empty
5	650	0.73	0.80	71	empty

Interfaces

36 interfaces between chains.

L–G · 1724 Å² buried · 12 hydrogen bonds · protein-protein
O–J · 1716 Å² buried · 10 hydrogen bonds · protein-protein
M–H · 1707 Å² buried · 12 hydrogen bonds · protein-protein
K–F · 1675 Å² buried · 14 hydrogen bonds · protein-protein
N–S · 1604 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 25 disulfide (disulfide).

Compared structures

5X8L · PD-L1 in complex with atezolizumab · 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 5X8L · PDBe 5X8L · UniProt Q9NZQ7

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