Research workbench
Structure of ester-hydrolase EH7 from metagenome of marine sediments at milazzo harbor (sicily, italy) complexed with a derivative of methyl 4-nitrophenyl hexylphosphonate
Analyse Structure of ester-hydrolase EH7 from metagenome of marine sediments at milazzo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PP8
- Type
- protein
- Length
- 3,212 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- UniProt
- A0A2K8JQ66
- Ligands
- MHH
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Esterase | protein | 402 | 36% helix, 21% strand | A0A2K8JQ66 |
| B, D, F, H | Esterase | protein | 401 | 36% helix, 21% strand | A0A2K8JQ66 |
Ligands and binding sites
- MHH · methyl hydrogen (R)-hexylphosphonate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 6 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.78 | 0.80 | 112 | PEG, MHH |
| 2 | 816 | 0.77 | 0.80 | 81 | MHH |
| 3 | 883 | 0.76 | 0.80 | 99 | GOL, MHH |
| 4 | 1145 | 0.76 | 0.78 | 118 | MHH |
| 5 | 776 | 0.76 | 0.80 | 81 | MHH |
Interfaces
12 interfaces between chains.
- G–H · 1086 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1085 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1084 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1070 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 1069 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7PP8 · Structure of ester-hydrolase EH7 from metagenome of marine sediments at milazzo harbor… · 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 A0A2K8JQ66
- Elsewhere: RCSB PDB 7PP8 · PDBe 7PP8 · UniProt A0A2K8JQ66
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