MolNFT v1 · #124276 · protein
Protein tyrosine phosphatase 1B N193A mutant in complex with TCS401, closed state
5KAD · Tyrosine-protein phosphatase non-receptor type 1: “Protein tyrosine phosphatase 1B N193A mutant in complex with TCS401, closed state”. X-ray diffraction, 2 ligands (OTA, CL), 4 pockets (best druggability 0.75). MolNFT v1 #124276 on…
- PDB
- 5KAD
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 1
- EC
- 3.1.3.48
- UniProt
- P18031
- Ligands
- OTA, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) | protein | 285 | 36% helix, 23% strand | P18031 |
| B | Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) | protein | 282 | 36% helix, 23% strand | P18031 |
Ligands and binding sites
- OTA · 2-(oxalyl-amino)-4,5,6,7-tetrahydro-thieno[2,3-c]pyridine-3-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.75 | 0.78 | 66 | empty |
| 2 | 129 | 0.47 | 0.78 | 25 | empty |
| 3 | 53 | 0.38 | 0.80 | 17 | OTA |
| 4 | 65 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5KAD · Protein Tyrosine Phosphatase 1B N193A mutant in complex with TCS401, closed state · 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 P18031
- Elsewhere: RCSB PDB 5KAD · PDBe 5KAD · UniProt P18031
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