Research workbench
Crystal structure of mgs-MILE3, an ALPHA/BETA hydrolase enzyme from the metagenome of pyrene-phenanthrene enrichment culture with sediment sample of milazzo harbor, italy
Analyse Crystal structure of mgs-MILE3, an ALPHA/BETA hydrolase enzyme from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JD5
- Type
- protein
- Length
- 1,267 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mgs-MILE3
- Ligands
- CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Mgs-MILE3 | protein | 317 | 43% helix, 18% strand | — |
| B | Mgs-MILE3 | protein | 318 | 43% helix, 18% strand | — |
| C | Mgs-MILE3 | protein | 315 | 43% helix, 18% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.81 | 0.86 | 59 | empty |
| 2 | 753 | 0.81 | 0.84 | 64 | empty |
| 3 | 724 | 0.80 | 0.84 | 61 | empty |
| 4 | 646 | 0.80 | 0.85 | 50 | empty |
| 5 | 715 | 0.67 | 0.75 | 60 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1036 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 1026 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 213 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 123 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5JD5 · Crystal structure of MGS-MilE3, an alpha/beta hydrolase enzyme from the metagenome of… · 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
- Elsewhere: RCSB PDB 5JD5 · PDBe 5JD5
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