Research workbench
Crystal structure of S. aureus pyruvate carboxylase in complex with coenzyme a
Analyse Crystal structure of S. aureus pyruvate carboxylase in complex with coenzyme a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HO8
- Type
- protein
- Length
- 3,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase
- UniProt
- Q99UY8
- Ligands
- COA, BTI, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase | protein | 994 | 37% helix, 17% strand | Q99UY8 |
| D | Pyruvate carboxylase | protein | 934 | 34% helix, 18% strand | Q99UY8 |
| C | Pyruvate carboxylase | protein | 995 | 39% helix, 18% strand | Q99UY8 |
| B | Pyruvate carboxylase | protein | 989 | 42% helix, 18% strand | Q99UY8 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, C, D, B
- BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · 2 copies · chains C, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.84 | 0.87 | 88 | empty |
| 2 | 752 | 0.84 | 0.87 | 95 | empty |
| 3 | 866 | 0.79 | 0.82 | 75 | empty |
| 4 | 339 | 0.77 | 0.88 | 51 | empty |
| 5 | 273 | 0.76 | 0.89 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2738 Ų buried · 52 hydrogen bonds · protein-protein
- D–B · 2645 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 1537 Ų buried · 19 hydrogen bonds · protein-protein
- C–B · 1480 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3HO8 · Crystal Structure of S. aureus Pyruvate Carboxylase in complex with Coenzyme A · 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 Q99UY8
- Elsewhere: RCSB PDB 3HO8 · PDBe 3HO8 · UniProt Q99UY8
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