Research workbench
Crystal structure of putative hydrolase (YP_751971.1) from shewanella frigidimarina ncimb 400 at 1.80 a resolution
Analyse Crystal structure of putative hydrolase (YP_751971.1) from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LHO
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydrolase
- UniProt
- Q07XY2
- Ligands
- NI, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative hydrolase | protein | 254 | 36% helix, 26% strand | Q07XY2 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.62 | 0.77 | 38 | NI, GOL, PEG |
| 2 | 95 | 0.42 | 0.77 | 15 | empty |
| 3 | 91 | 0.39 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3LHO · Crystal structure of putative hydrolase (YP_751971.1) from Shewanella frigidimarina NCIMB… · 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 Q07XY2
- Elsewhere: RCSB PDB 3LHO · PDBe 3LHO · UniProt Q07XY2
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