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Crystal structure of an encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor TNP470 bound
Analyse Crystal structure of an encephalitozoon cuniculi methionine aminopeptidase type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FMR
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine aminopeptidase 2
- EC
- 3.4.11.18
- UniProt
- Q8SR45
- Ligands
- TN4, FE, SO4
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine aminopeptidase 2 (EC 3.4.11.18) | protein | 356 | 29% helix, 27% strand | Q8SR45 |
Ligands and binding sites
- TN4 · (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.86 | 0.88 | 62 | empty |
| 2 | 277 | 0.67 | 0.83 | 37 | TN4 |
| 3 | 267 | 0.67 | 0.83 | 38 | TN4 |
| 4 | 141 | 0.45 | 0.77 | 19 | empty |
| 5 | 112 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 847 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3FMR · Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SR45 · AlphaFold monomer V2.0 prediction for methionine aminopeptidase 2 (Q8SR45) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8SR45
- Elsewhere: RCSB PDB 3FMR · PDBe 3FMR · UniProt Q8SR45
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