MolNFT v1 · #4922 · protein

HPT + HMTT

1E2N · Thymidine kinase: “HPT + HMTT”. X-ray diffraction, 2 ligands (RCA, SO4), 9 pockets (best druggability 0.82). MolNFT v1 #4922 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1E2N
Type: protein
Length: 619 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidine kinase
EC: 2.7.1.21
UniProt: P03176
Ligands: RCA, SO4
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidine kinase (EC 2.7.1.21)	protein	310	57% helix, 13% strand	P03176
B	Thymidine kinase (EC 2.7.1.21)	protein	309	57% helix, 12% strand	P03176

Ligands and binding sites

RCA · 6-{[4-(hydroxymethyl)-5-methyl-2,6-dioxohexahydropyrimidin-5-yl]methyl}-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

9 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	203	0.82	0.96	38	SO4, RCA
2	171	0.58	0.81	26	SO4, RCA
3	172	0.54	0.79	30	empty
4	102	0.46	0.80	22	empty
5	108	0.44	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 1730 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1E2N · HPT + HMTT · the same entry in another collection · 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 P03176
Elsewhere: RCSB PDB 1E2N · PDBe 1E2N · UniProt P03176

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