MolNFT v1 · #140863 · protein

Hd domain-containing protein YGK1(YGL101W)

5YOX · Hd domain-containing protein YGL101W: “Hd domain-containing protein YGK1(YGL101W)”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.78). MolNFT v1 #140863 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5YOX
Type: protein
Length: 1,406 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hd domain-containing protein YGL101W
UniProt: P53144
Ligands: ZN
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hd domain-containing protein YGL101W	protein	183	64% helix, 0% strand	P53144
B	Hd domain-containing protein YGL101W	protein	174	72% helix, 0% strand	P53144
C, H	Hd domain-containing protein YGL101W	protein	175	63% helix, 0% strand	P53144
D, E	Hd domain-containing protein YGL101W	protein	176	68% helix, 0% strand	P53144
F	Hd domain-containing protein YGL101W	protein	174	64% helix, 0% strand	P53144
G	Hd domain-containing protein YGL101W	protein	173	65% helix, 0% strand	P53144

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

14 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	995	0.78	0.80	89	empty
2	807	0.74	0.79	72	empty
3	654	0.64	0.74	36	empty
4	150	0.51	0.79	20	empty
5	226	0.49	0.75	32	empty

Interfaces

14 interfaces between chains.

B–C · 2364 Å² buried · 25 hydrogen bonds · protein-protein
A–G · 2324 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2322 Å² buried · 20 hydrogen bonds · protein-protein
D–H · 2220 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 475 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified (engineered).

Compared structures

5YOX · HD domain-containing protein YGK1(YGL101W) · the same entry in another collection · chain H against H, TM-score 1.00
P53144 · AlphaFold monomer V2.0 prediction for 5'-deoxynucleotidase YGK1 (P53144) · a predicted model of the same protein · chain F 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 P53144
Elsewhere: RCSB PDB 5YOX · PDBe 5YOX · UniProt P53144

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