Research workbench
Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A
Analyse Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCN
- Type
- protein
- Length
- 1,797 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Planctopirus limnophila DSM 3776
- Molecule
- Serine O-acetyltransferase
- EC
- 2.3.1.30
- UniProt
- D5SUT9
- Ligands
- CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.15 · 6 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine O-acetyltransferase (EC 2.3.1.30) | protein | 296 | 46% helix, 14% strand | D5SUT9 |
| B | Serine O-acetyltransferase (EC 2.3.1.30) | protein | 306 | 45% helix, 13% strand | D5SUT9 |
| C | Serine O-acetyltransferase (EC 2.3.1.30) | protein | 294 | 45% helix, 13% strand | D5SUT9 |
| D | Serine O-acetyltransferase (EC 2.3.1.30) | protein | 298 | 46% helix, 13% strand | D5SUT9 |
| E | Serine O-acetyltransferase (EC 2.3.1.30) | protein | 294 | 46% helix, 13% strand | D5SUT9 |
| F | Serine O-acetyltransferase (EC 2.3.1.30) | protein | 309 | 45% helix, 13% strand | D5SUT9 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, E, C, D
- GOL · Glycerol · additive · 6 copies · chains A, E, C, D, F
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.80 | 0.82 | 84 | PEG, GOL |
| 2 | 647 | 0.80 | 0.85 | 49 | empty |
| 3 | 924 | 0.79 | 0.81 | 82 | GOL |
| 4 | 609 | 0.79 | 0.84 | 47 | GOL |
| 5 | 1007 | 0.76 | 0.78 | 72 | empty |
Interfaces
15 interfaces between chains.
- A–F · 3292 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 3249 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 2868 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2848 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2848 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6LCN · Crystal structure of serine acetyltransferase from planctomyces limnophilus at 2.15A · 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 D5SUT9
- Elsewhere: RCSB PDB 6LCN · PDBe 6LCN · UniProt D5SUT9
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