Research workbench
Crystal structure of the glycopeptide antibiotic sulfotransferase stal complexed with A3P and desulfo-A47934.
Analyse Crystal structure of the glycopeptide antibiotic sulfotransferase stal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EEC
- Type
- protein
- Length
- 502 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stal; Desulfo-A47934
- UniProt
- Q8KLM3
- Ligands
- A3P
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stal | protein | 253 | 51% helix, 10% strand | Q8KLM3 |
| B | Stal | protein | 242 | 50% helix, 11% strand | Q8KLM3 |
| C | Desulfo-A47934 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.68 | 0.83 | 37 | A3P |
| 2 | 441 | 0.64 | 0.78 | 51 | empty |
| 3 | 89 | 0.52 | 0.83 | 19 | empty |
| 4 | 148 | 0.45 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 767 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 550 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 2 disulfide (nonstandard, disulfide).
Compared structures
- 4EEC · Crystal Structure of the glycopeptide antibiotic sulfotransferase StaL complexed with A3P… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8KLM3 · AlphaFold monomer V2.0 prediction for desulfo-A47934 sulfotransferase (Q8KLM3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8KLM3
- Elsewhere: RCSB PDB 4EEC · PDBe 4EEC · UniProt Q8KLM3
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