MolNFT v1 · #112279 · protein

Hit like protein

4ZGL · Uncharacterized hit-like protein HP_0404: “Hit like protein”. X-ray diffraction, 1 ligand (AMP), 18 pockets (best druggability 0.73). MolNFT v1 #112279 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ZGL
Type: protein
Length: 995 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized hit-like protein HP_0404
UniProt: P64382
Ligands: AMP
Pockets: 18 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, G, H, J	Uncharacterized hit-like protein HP_0404	protein	101	31% helix, 27% strand	P64382
D, F, I	Uncharacterized hit-like protein HP_0404	protein	102	29% helix, 26% strand	P64382
E	Uncharacterized hit-like protein HP_0404	protein	83	7% helix, 33% strand	P64382

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 5 copies · chains B, C, F, H, I

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

Pockets

18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.73	0.97	27	empty
2	53	0.70	0.98	19	empty
3	71	0.66	0.94	23	empty
4	157	0.51	0.78	28	empty
5	160	0.43	0.74	28	AMP

Interfaces

17 interfaces between chains.

C–D · 1144 Å² buried · 16 hydrogen bonds · protein-protein
I–J · 1130 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1092 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1089 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 997 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4ZGL · Hit Like Protein · the same entry in another collection · chain J against J, TM-score 1.00
P64382 · AlphaFold monomer V2.0 prediction for uncharacterized hit-like protein HP_0404 (P64382) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P64382
Elsewhere: RCSB PDB 4ZGL · PDBe 4ZGL · UniProt P64382

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