MolNFT v1 · #139211 · protein

Pd-L1 in complex with durvalumab

5X8M · Programmed cell death 1 ligand 1: “Pd-L1 in complex with durvalumab”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #139211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X8M
Type: protein
Length: 543 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death 1 ligand 1; Durvalumab heavy chain; Durvalumab light chain
UniProt: Q9NZQ7
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death 1 ligand 1	protein	116	9% helix, 49% strand	Q9NZQ7
B	Durvalumab heavy chain	protein	214	7% helix, 52% strand	—
C	Durvalumab light chain	protein	213	7% helix, 50% strand	—

Pockets

5 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	508	0.62	0.75	55	empty
2	109	0.37	0.74	26	empty
3	105	0.36	0.74	22	empty
4	80	0.34	0.75	15	empty
5	51	0.25	0.73	13	empty

Interfaces

3 interfaces between chains.

B–C · 1720 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 505 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 377 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5X8M · PD-L1 in complex with durvalumab · 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 5X8M · PDBe 5X8M · UniProt Q9NZQ7

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