MolNFT v1 · #119836 · protein

Pd-1 in complex with nivolumab Fab

5GGR · Heavy chain: “Pd-1 in complex with nivolumab Fab”. X-ray diffraction, 14 pockets (best druggability 0.57). MolNFT v1 #119836 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GGR
Type: protein
Length: 1,075 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: 14 · best druggability 0.57

Structure

x-ray diffraction · 5 distinct chains · 3% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy chain	protein	209	4% helix, 52% strand	—
B, L	Light chain	protein	212	7% helix, 50% strand	—
H	Heavy chain	protein	207	3% helix, 55% strand	—
Y	Programmed cell death protein 1	protein	118	0% helix, 44% strand	Q15116
Z	Programmed cell death protein 1	protein	117	0% helix, 49% strand	Q15116

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.57	0.73	52	empty
2	394	0.57	0.74	53	empty
3	377	0.56	0.74	50	empty
4	189	0.55	0.80	34	empty
5	85	0.55	0.86	23	empty

Interfaces

8 interfaces between chains.

A–B · 1603 Å² buried · 11 hydrogen bonds · protein-protein
H–L · 1549 Å² buried · 12 hydrogen bonds · protein-protein
H–Z · 618 Å² buried · 8 hydrogen bonds · protein-protein
A–Y · 607 Å² buried · 8 hydrogen bonds · protein-protein
B–Y · 254 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5GGR · PD-1 in complex with nivolumab 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 Z against A, TM-score 0.93

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 5GGR · PDBe 5GGR · UniProt Q15116

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