Research workbench
The crystal structure of carboxyltransferase from staphylococcus aureus bound to the antimicrobial agent moiramide B.
Analyse The crystal structure of carboxyltransferase from staphylococcus aureus bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KDR
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-coenzyme a carboxylase carboxyl transferase subunit alpha; Acetyl-coenzyme a…
- EC
- 6.4.1.2
- UniProt
- Q2FG38, Q2YTE0
- Ligands
- YT5, ZN, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-coenzyme a carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) | protein | 301 | 50% helix, 16% strand | Q2FG38 |
| B | Acetyl-coenzyme a carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) | protein | 250 | 40% helix, 22% strand | Q2YTE0 |
Ligands and binding sites
- YT5 · Moiramide B · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.73 | 0.85 | 52 | YT5 |
| 2 | 50 | 0.65 | 0.95 | 20 | empty |
| 3 | 60 | 0.46 | 0.84 | 23 | EDO |
| 4 | 69 | 0.45 | 0.83 | 13 | empty |
| 5 | 50 | 0.34 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2410 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5KDR · The crystal structure of carboxyltransferase from Staphylococcus Aureus bound to the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FG38 · AlphaFold monomer V2.0 prediction for acetyl-coenzyme a carboxylase carboxyl transferase… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q2YTE0 · AlphaFold monomer V2.0 prediction for acetyl-coenzyme a carboxylase carboxyl transferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q2FG38
- Every structure of UniProt Q2YTE0
- Elsewhere: RCSB PDB 5KDR · PDBe 5KDR · UniProt Q2FG38 · UniProt Q2YTE0
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