MolNFT v1 · #87674 · protein
Crystal structure of carboxylesterase LPEST1 from lactobacillus plantarum: high resolution model
4C89: “Crystal structure of carboxylesterase LPEST1 from lactobacillus plantarum: high resolution model”. X-ray diffraction, 9 pockets (best druggability 0.85). MolNFT v1 #87674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4C89
- Type
- protein
- Length
- 1,362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- EC
- 3.1.1.1
- UniProt
- Q88Y25
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Esterase (EC 3.1.1.1) | protein | 341 | 36% helix, 20% strand | Q88Y25 |
| C | Esterase (EC 3.1.1.1) | protein | 339 | 37% helix, 20% strand | Q88Y25 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- MLI · Malonate ion · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.85 | 0.86 | 109 | empty |
| 2 | 1007 | 0.80 | 0.81 | 82 | empty |
| 3 | 454 | 0.70 | 0.80 | 41 | GOL |
| 4 | 464 | 0.69 | 0.80 | 39 | empty |
| 5 | 271 | 0.50 | 0.74 | 42 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1120 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 917 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 446 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 163 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4C89 · Crystal structure of carboxylesterase LpEst1 from Lactobacillus plantarum: high… · the same entry in another collection · chain A 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 Q88Y25
- Elsewhere: RCSB PDB 4C89 · PDBe 4C89 · UniProt Q88Y25
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