Research workbench
Crystal structure of staphylococcus aureus pyruvate carboxylase
Analyse Crystal structure of staphylococcus aureus pyruvate carboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BG5
- Type
- protein
- Length
- 4,345 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase
- UniProt
- Q99UY8
- Ligands
- BTI, PYR, ATP, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase | protein | 1137 | 38% helix, 20% strand | Q99UY8 |
| B | Pyruvate carboxylase | protein | 1074 | 38% helix, 20% strand | Q99UY8 |
| C | Pyruvate carboxylase | protein | 1067 | 40% helix, 19% strand | Q99UY8 |
| D | Pyruvate carboxylase | protein | 1067 | 39% helix, 19% strand | Q99UY8 |
Ligands and binding sites
- BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
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 | 797 | 0.85 | 0.87 | 93 | empty |
| 2 | 675 | 0.84 | 0.88 | 87 | empty |
| 3 | 935 | 0.82 | 0.83 | 85 | ATP |
| 4 | 670 | 0.79 | 0.84 | 71 | empty |
| 5 | 137 | 0.79 | 0.96 | 32 | MN, PYR, BTI |
Interfaces
6 interfaces between chains.
- B–D · 2820 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2788 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1620 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1545 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1130 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (biotinylation).
Compared structures
- 3BG5 · Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase · 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 3BG5 · PDBe 3BG5 · UniProt Q99UY8
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