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Complex structure of PD1 and 609A-Fab

Analyse Complex structure of PD1 and 609A-Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VUX
Type: protein
Length: 551 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death protein 1; Heavy chain of Fab fragment; Light chain of Fab fragment
UniProt: Q15116
Ligands: THR, MG, CL
Pockets: 9 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death protein 1	protein	122	2% helix, 49% strand	Q15116
H	Heavy chain of Fab fragment	protein	216	9% helix, 51% strand	—
L	Light chain of Fab fragment	protein	213	5% helix, 51% strand	—

Ligands and binding sites

THR · Threonine · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A, H, L
CL · Chloride ion · ion · chains L
GOL · Glycerol · additive · 7 copies · chains A, H, L
EDO · 1,2-ethanediol · additive · 7 copies · chains A, H, L
PEG · Di(hydroxyethyl)ether · additive · chains L

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.53	0.89	19	EDO, MG
2	107	0.52	0.82	22	GOL
3	277	0.51	0.74	42	GOL
4	154	0.47	0.77	22	EDO
5	176	0.44	0.74	26	MG

Interfaces

3 interfaces between chains.

H–L · 1792 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 638 Å² buried · 13 hydrogen bonds · protein-protein
A–L · 421 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

7VUX · Complex structure of PD1 and 609A-Fab · the same entry in another collection · chain A against A, TM-score 1.00
Q15116 · AlphaFold monomer V2.0 prediction for programmed cell death protein 1 (Q15116) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q15116
Elsewhere: RCSB PDB 7VUX · PDBe 7VUX · UniProt Q15116

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