MolNFT v1 · #151265 · protein

Hpd-1/NBO1A Fab complex

6HIG · Heavy chain: “Hpd-1/NBO1A Fab complex”. X-ray diffraction, 5 pockets (best druggability 0.48). MolNFT v1 #151265 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HIG
Type: protein
Length: 499 residues
Chains: 3
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: 5 · best druggability 0.48

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Heavy chain	protein	209	9% helix, 53% strand	—
L	Light chain	protein	203	7% helix, 53% strand	—
B	Programmed cell death protein 1	protein	87	3% helix, 56% strand	Q15116

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.48	0.74	33	empty
2	84	0.39	0.77	23	empty
3	64	0.35	0.77	14	empty
4	52	0.30	0.76	16	empty
5	52	0.28	0.74	17	empty

Interfaces

3 interfaces between chains.

H–L · 1725 Å² buried · 15 hydrogen bonds · protein-protein
H–B · 551 Å² buried · 8 hydrogen bonds · protein-protein
L–B · 295 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6HIG · hPD-1/NBO1a Fab complex · the same entry in another collection · chain H against H, 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 B against A, TM-score 0.98

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 6HIG · PDBe 6HIG · UniProt Q15116

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.