MolNFT v1 · #126956 · protein
Crystal structure of carboxyl esterase 2 (TMELEST2) from mycorrhizal fungus tuber melanosporum
5MIF · 'carboxyl esterase 2: “Crystal structure of carboxyl esterase 2 (TMELEST2) from mycorrhizal fungus tuber melanosporum”. X-ray diffraction, 1 ligand (TRT), 7 pockets (best druggability 0.75). MolNFT v1 #126956 on GenesisL1: 3D…
- PDB
- 5MIF
- Type
- protein
- Length
- 1,206 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 'carboxyl esterase 2
- UniProt
- D5GA36
- Ligands
- TRT
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 'carboxyl esterase 2 | protein | 302 | 40% helix, 21% strand | D5GA36 |
| C | 'carboxyl esterase 2 | protein | 301 | 38% helix, 21% strand | D5GA36 |
| D | 'carboxyl esterase 2 | protein | 301 | 39% helix, 21% strand | D5GA36 |
Ligands and binding sites
- TRT · Fragment of triton X-100 · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.75 | 0.82 | 54 | empty |
| 2 | 578 | 0.75 | 0.82 | 55 | TRT |
| 3 | 576 | 0.75 | 0.82 | 53 | empty |
| 4 | 583 | 0.75 | 0.82 | 56 | TRT |
| 5 | 866 | 0.72 | 0.77 | 104 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1378 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1365 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5MIF · Crystal structure of carboxyl esterase 2 (TmelEST2) from mycorrhizal fungus Tuber… · the same entry in another collection · chain B against B, 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 D5GA36
- Elsewhere: RCSB PDB 5MIF · PDBe 5MIF · UniProt D5GA36
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