Research workbench
Structure of ester-hydrolase EH7 from the metagenome of marine sediments at milazzo harbor (sicily, italy)
Analyse Structure of ester-hydrolase EH7 from the metagenome of marine sediments at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PP3
- Type
- protein
- Length
- 1,606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- UniProt
- A0A2K8JQ66
- Ligands
- CL
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Esterase | protein | 402 | 36% helix, 21% strand | A0A2K8JQ66 |
| B, D | Esterase | protein | 401 | 36% helix, 21% strand | A0A2K8JQ66 |
Ligands and binding sites
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.75 | 0.81 | 80 | GOL |
| 2 | 716 | 0.74 | 0.80 | 85 | GOL |
| 3 | 777 | 0.74 | 0.79 | 93 | PEG, GOL |
| 4 | 579 | 0.72 | 0.80 | 76 | GOL |
| 5 | 314 | 0.58 | 0.77 | 31 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 1073 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1073 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1063 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1061 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7PP3 · Structure of ester-hydrolase EH7 from the metagenome of marine sediments at milazzo… · 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 A0A2K8JQ66
- Elsewhere: RCSB PDB 7PP3 · PDBe 7PP3 · UniProt A0A2K8JQ66
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