MolNFT v1 · #6664 · protein
Protein SERINE/THREONINE phosphatase-1 (alpha isoform, type 1) complexed with microcystin-lr toxin
1FJM: “Protein SERINE/THREONINE phosphatase-1 (alpha isoform, type 1) complexed with microcystin-lr toxin”. X-ray diffraction, 4 ligands (1ZN, FGA, DAM), 3 pockets (best druggability 0.72). MolNFT v1 #6664 on GenesisL1: 3D structure…
- PDB
- 1FJM
- Type
- protein
- Length
- 591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SERINE/THREONINE phosphatase-1 (alpha isoform, type 1); Microcystin lr
- EC
- 3.1.3.16
- UniProt
- P08129
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SERINE/THREONINE phosphatase-1 (alpha isoform, type 1) (EC 3.1.3.16) | protein | 294 | 35% helix, 19% strand | P08129 |
| B | Protein SERINE/THREONINE phosphatase-1 (alpha isoform, type 1) (EC 3.1.3.16) | protein | 289 | 34% helix, 19% strand | P08129 |
| M, N | 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 · 2 copies · chains A, M, B, N
- FGA · Gamma-D-glutamic acid · ligand · 2 copies · chains A, M, B, N
- DAM · N-methyl-alpha-beta-dehydroalanine · ligand · 2 copies · chains A, M, B, N
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.72 | 0.77 | 71 | empty |
| 2 | 276 | 0.59 | 0.79 | 38 | FGA, DAM |
| 3 | 225 | 0.58 | 0.79 | 29 | FGA, DAM |
Interfaces
3 interfaces between chains.
- A–M · 271 Ų buried · 3 hydrogen bonds · protein-protein
- B–N · 270 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 211 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 2 d-amino, 2 modified (covalent ligand, additive adduct, D-amino acid, nonstandard).
Compared structures
- 1FJM · Protein serine/threonine phosphatase-1 (alpha isoform, type 1) complexed with… · 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 P08129
- Elsewhere: RCSB PDB 1FJM · PDBe 1FJM · UniProt P08129
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