MolNFT v1 · #123599 · protein
SERINE/THREONINE phosphatase Z1 (candida albicans) binds to inhibitor microcystin-lr
5JPF · SERINE/THREONINE-protein phosphatase: “SERINE/THREONINE phosphatase Z1 (candida albicans) binds to inhibitor microcystin-lr”. X-ray diffraction, 4 ligands (1ZN, FGA, DAM), 2 pockets (best druggability 0.53). MolNFT v1 #123599 on…
- PDB
- 5JPF
- Type
- protein
- Length
- 294 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase; Microcystin-lr
- EC
- 3.1.3.16
- UniProt
- C4YM68
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein phosphatase (EC 3.1.3.16) | protein | 290 | 36% helix, 20% strand | C4YM68 |
| M | Microcystin-lr | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1ZN · (2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid · ligand · chains A, M
- FGA · Gamma-D-glutamic acid · ligand · chains A, M
- DAM · N-methyl-alpha-beta-dehydroalanine · ligand · chains A, M
- MN · Manganese (II) ion · metal · 2 copies · chains A
- MLI · Malonate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.53 | 0.78 | 34 | 1ZN, FGA, MN, MLI |
| 2 | 73 | 0.31 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–M · 237 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 5JPF · Serine/Threonine phosphatase Z1 (Candida albicans) binds to inhibitor microcystin-LR · the same entry in another collection · chain M against M, 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 C4YM68
- Elsewhere: RCSB PDB 5JPF · PDBe 5JPF · UniProt C4YM68
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