MolNFT v1 · #27517 · protein
Crystal structure of human prl-1
1XM2 · Tyrosine phosphatase: “Crystal structure of human prl-1”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.71). MolNFT v1 #27517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XM2
- Type
- protein
- Length
- 887 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine phosphatase
- EC
- 3.1.3.48
- UniProt
- Q93096
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Tyrosine phosphatase (EC 3.1.3.48) | protein | 149 | 42% helix, 16% strand | Q93096 |
| D | Tyrosine phosphatase (EC 3.1.3.48) | protein | 144 | 44% helix, 17% strand | Q93096 |
| F | Tyrosine phosphatase (EC 3.1.3.48) | protein | 147 | 41% helix, 16% strand | Q93096 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.71 | 0.79 | 47 | empty |
| 2 | 593 | 0.69 | 0.77 | 45 | empty |
| 3 | 412 | 0.61 | 0.76 | 46 | empty |
| 4 | 264 | 0.52 | 0.75 | 38 | empty |
| 5 | 217 | 0.48 | 0.75 | 39 | empty |
Interfaces
9 interfaces between chains.
- B–F · 703 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 581 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 575 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 571 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
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 Q93096
- Elsewhere: RCSB PDB 1XM2 · PDBe 1XM2 · UniProt Q93096
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