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Complex structure of gy-14 and pd-1

Analyse Complex structure of gy-14 and pd-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6J14
Type: protein
Length: 325 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gy-14 heavy chain V fragment; Gy-14 light chain V fragment; Programmed cell death protein…
UniProt: Q15116
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gy-14 heavy chain V fragment	protein	113	5% helix, 56% strand	—
B	Gy-14 light chain V fragment	protein	112	3% helix, 47% strand	—
G	Programmed cell death protein 1	protein	100	3% helix, 57% strand	Q15116

Pockets

2 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	240	0.51	0.75	38	empty
2	86	0.36	0.75	18	empty

Interfaces

3 interfaces between chains.

A–B · 887 Å² buried · 10 hydrogen bonds · protein-protein
A–G · 527 Å² buried · 11 hydrogen bonds · protein-protein
B–G · 224 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6J14 · Complex structure of GY-14 and PD-1 · 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 G against A, TM-score 0.95

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 6J14 · PDBe 6J14 · UniProt Q15116

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