MolNFT v1 · #78890 · protein

Human pantothenate kinase 3 in complex with a pantothenate analog

3SMS: “Human pantothenate kinase 3 in complex with a pantothenate analog”. X-ray diffraction, 3 ligands (ADP, RNH, UNX), 5 pockets (best druggability 0.67). MolNFT v1 #78890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SMS
Type: protein
Length: 351 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pantothenate kinase 3
EC: 2.7.1.33
UniProt: Q9H999
Ligands: ADP, RNH, UNX
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pantothenate kinase 3 (EC 2.7.1.33)	protein	351	42% helix, 26% strand	Q9H999

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
RNH · (2R)-N-[3-(heptylamino)-3-oxopropyl]-2,4-dihydroxy-3,3-dimethylbutanamide · ligand · chains A
UNX · Unknown atom or ion · ion · 11 copies · chains A

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

Pockets

5 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	242	0.67	0.83	30	UNX
2	284	0.65	0.82	41	ADP, UNX
3	273	0.54	0.75	31	UNX
4	127	0.48	0.78	15	empty
5	52	0.40	0.82	18	empty

Compared structures

3SMS · Human Pantothenate kinase 3 in complex with a pantothenate analog · the same entry in another collection · chain A against A, TM-score 1.00
Q9H999 · AlphaFold monomer V2.0 prediction for pantothenate kinase 3 (Q9H999) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q9H999
Elsewhere: RCSB PDB 3SMS · PDBe 3SMS · UniProt Q9H999

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