MolNFT v1 · #141371 · protein

Crystal structure of tk-ptp in the active form

5Z5A · Protein-tyrosine phosphatase: “Crystal structure of tk-ptp in the active form”. X-ray diffraction, 1 ligand (VN3), 2 pockets (best druggability 0.45). MolNFT v1 #141371 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z5A
Type: protein
Length: 442 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-tyrosine phosphatase
UniProt: Q8X270
Ligands: VN3
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein-tyrosine phosphatase	protein	148	49% helix, 12% strand	Q8X270
B, C	Protein-tyrosine phosphatase	protein	147	49% helix, 12% strand	Q8X270

Ligands and binding sites

VN3 · Vanadate ion · ligand · 3 copies · chains A, B, C

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

Pockets

2 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	69	0.45	0.82	17	empty
2	127	0.36	0.72	17	empty

Interfaces

2 interfaces between chains.

A–B · 500 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 64 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5Z5A · Crystal structure of Tk-PTP in the active form · 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 Q8X270
Elsewhere: RCSB PDB 5Z5A · PDBe 5Z5A · UniProt Q8X270

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