MolNFT v1 · #139547 · protein

Complex structure of durvalumab-SCFV/PD-L1

5XJ4 · Programmed cell death 1 ligand 1: “Complex structure of durvalumab-SCFV/PD-L1”. X-ray diffraction, 5 pockets (best druggability 0.43). MolNFT v1 #139547 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XJ4
Type: protein
Length: 439 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death 1 ligand 1; Durvalumab-vh; Durvalumab-vl
UniProt: Q9NZQ7
Pockets: 5 · best druggability 0.43

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	206	7% helix, 53% strand	Q9NZQ7
H	Durvalumab-vh	protein	120	8% helix, 51% strand	—
L	Durvalumab-vl	protein	113	5% helix, 48% strand	—

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.43	0.76	20	empty
2	117	0.40	0.75	22	empty
3	64	0.32	0.76	15	empty
4	57	0.30	0.76	14	empty
5	53	0.29	0.76	16	empty

Interfaces

3 interfaces between chains.

H–L · 789 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 527 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 365 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5XJ4 · Complex structure of durvalumab-scFv/PD-L1 · 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 5XJ4 · PDBe 5XJ4 · UniProt Q9NZQ7

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