Research workbench
Crystal structure of human protein phosphatase 5C (PP5C) in complex with a triazole inhibitor
Analyse Crystal structure of human protein phosphatase 5C (PP5C) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UI1
- Type
- protein
- Length
- 1,253 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase 5
- EC
- 3.1.3.16
- UniProt
- P53041
- Ligands
- 8D4, MN
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 312 | 35% helix, 20% strand | P53041 |
| B | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 313 | 35% helix, 20% strand | P53041 |
| C | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 317 | 33% helix, 20% strand | P53041 |
| D | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 311 | 35% helix, 22% strand | P53041 |
Ligands and binding sites
- 8D4 · 5-phenyl-1H-1,2,3-triazole-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.70 | 0.77 | 59 | 8D4 |
| 2 | 402 | 0.59 | 0.75 | 43 | empty |
| 3 | 367 | 0.57 | 0.75 | 44 | empty |
| 4 | 202 | 0.50 | 0.76 | 26 | empty |
| 5 | 86 | 0.36 | 0.75 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–B · 250 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 235 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 124 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 81 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5UI1 · Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole… · the same entry in another collection · chain D against D, TM-score 1.00
- P53041 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 5 (P53041) · a predicted model of the same protein · chain B 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 P53041
- Elsewhere: RCSB PDB 5UI1 · PDBe 5UI1 · UniProt P53041
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