Research workbench
Crystal structure of a putative esterase from staphylococcus aureus
Analyse Crystal structure of a putative esterase from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D7R
- Type
- protein
- Length
- 591 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- EC
- 3.1.-.-
- UniProt
- A8Z540
- Ligands
- NA, BR, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Esterase (EC 3.1.-.-) | protein | 296 | 42% helix, 16% strand | A8Z540 |
| B | Esterase (EC 3.1.-.-) | protein | 295 | 42% helix, 16% strand | A8Z540 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 20 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.76 | 0.93 | 26 | DMS |
| 2 | 153 | 0.74 | 0.92 | 26 | DMS |
| 3 | 130 | 0.46 | 0.78 | 24 | GOL |
| 4 | 125 | 0.46 | 0.78 | 19 | DMS |
| 5 | 143 | 0.44 | 0.76 | 18 | DMS |
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3D7R · Crystal structure of a putative esterase from Staphylococcus aureus · 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 A8Z540
- Elsewhere: RCSB PDB 3D7R · PDBe 3D7R · UniProt A8Z540
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