MolNFT v1 · #124387 · protein
The crystal structure of carboxyltransferase from staphylococcus aureus bound to the antimicrobial agent moiramide B.
5KDR · Acetyl-coenzyme a carboxylase carboxyl transferase subunit…: “The crystal structure of carboxyltransferase from staphylococcus aureus bound to the antimicrobial agent…”. X-ray diffraction, 3 ligands (YT5, ZN, SO4), 5 pockets (best…
- 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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