MolNFT v1 · #119837 · protein

Pd-1 in complex with pembrolizumab Fab

5GGS · Heavy chain: “Pd-1 in complex with pembrolizumab Fab”. X-ray diffraction, 10 pockets (best druggability 0.78). MolNFT v1 #119837 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GGS
Type: protein
Length: 1,100 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain; Light chain; Programmed cell death protein 1
UniProt: Q15116
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy chain	protein	219	12% helix, 50% strand	—
B, D	Light chain	protein	217	5% helix, 51% strand	—
C	Heavy chain	protein	220	10% helix, 51% strand	—
Y	Programmed cell death protein 1	protein	114	3% helix, 51% strand	Q15116
Z	Programmed cell death protein 1	protein	113	3% helix, 48% strand	Q15116

Pockets

10 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	505	0.78	0.85	84	empty
2	119	0.54	0.83	26	empty
3	111	0.52	0.82	21	empty
4	131	0.46	0.77	28	empty
5	92	0.41	0.78	23	empty

Interfaces

8 interfaces between chains.

A–B · 1926 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1894 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1161 Å² buried · 3 hydrogen bonds · protein-protein
A–Z · 758 Å² buried · 14 hydrogen bonds · protein-protein
C–Y · 747 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5GGS · PD-1 in complex with pembrolizumab Fab · the same entry in another collection · chain Z against Z, 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 Y against A, TM-score 0.96

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 5GGS · PDBe 5GGS · UniProt Q15116

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