MolNFT v1 · #58937 · protein

Crystal structure of the pd-1/PD-L1 complex

3BIK · Programmed cell death 1 ligand 1: “Crystal structure of the pd-1/PD-L1 complex”. X-ray diffraction, 1 pocket (best druggability 0.66). MolNFT v1 #58937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BIK
Type: protein
Length: 446 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death 1 ligand 1; Programmed cell death protein 1
UniProt: Q9NZQ7, Q02242
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death 1 ligand 1	protein	212	6% helix, 54% strand	Q9NZQ7
B	Programmed cell death protein 1	protein	116	3% helix, 56% strand	Q02242
C	Programmed cell death protein 1	protein	118	3% helix, 52% strand	Q02242

Ligands and binding sites

GOL · Glycerol · additive · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	486	0.66	0.78	51	empty

Interfaces

3 interfaces between chains.

A–B · 894 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 349 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 206 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3BIK · Crystal Structure of the PD-1/PD-L1 Complex · the same entry in another collection · chain A against A, TM-score 1.00
Q02242 · AlphaFold monomer V2.0 prediction for programmed cell death protein 1 (Q02242) · a predicted model of the same protein · chain B against A, TM-score 0.99

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
Every structure of UniProt Q02242
Elsewhere: RCSB PDB 3BIK · PDBe 3BIK · UniProt Q9NZQ7 · UniProt Q02242

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