MolNFT v1 · #112791 · protein
Co-crystal structures of PP5 in complex with 5-methyl-7- OXABICYCLO[2.2.1]HEPTANE-2,3-dicarboxylic acid
4ZVZ · SERINE/THREONINE-protein phosphatase 5: “Co-crystal structures of PP5 in complex with 5-methyl-7- OXABICYCLO[2.2.1]HEPTANE-2,3-dicarboxylic acid”. X-ray diffraction, 3 ligands (4TF, MN, NA), 8 pockets (best druggability 0.80).…
- PDB
- 4ZVZ
- Type
- protein
- Length
- 1,249 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
- 4TF, MN, NA
- Pockets
- 8 · best druggability 0.80
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 | 34% helix, 19% strand | P53041 |
| B | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 316 | 34% helix, 20% strand | P53041 |
| C | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 309 | 35% helix, 19% strand | P53041 |
| D | SERINE/THREONINE-protein phosphatase 5 (EC 3.1.3.16) | protein | 312 | 34% helix, 21% strand | P53041 |
Ligands and binding sites
- 4TF · (1R,2S,3R,4S,5S)-5-(propoxymethyl)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.80 | 0.82 | 82 | empty |
| 2 | 687 | 0.70 | 0.77 | 45 | empty |
| 3 | 174 | 0.41 | 0.73 | 27 | empty |
| 4 | 62 | 0.37 | 0.79 | 14 | 4TF |
| 5 | 69 | 0.35 | 0.76 | 17 | 4TF |
Interfaces
4 interfaces between chains.
- A–B · 688 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 277 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 207 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZVZ · Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicar… · 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 C 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 4ZVZ · PDBe 4ZVZ · UniProt P53041
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