Research workbench
Crystal structure of R54E mutant of S. aureus pyruvate carboxylase
Analyse Crystal structure of R54E mutant of S. 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
- 4HNV
- Type
- protein
- Length
- 4,300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase
- EC
- 6.4.1.1
- UniProt
- Q99UY8
- Ligands
- BTI, ADP, ATP, MN, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1133 | 38% helix, 20% strand | Q99UY8 |
| B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1033 | 39% helix, 19% strand | Q99UY8 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1067 | 40% helix, 18% strand | Q99UY8 |
| D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1067 | 38% 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
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains C
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, 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 | 1164 | 0.82 | 0.84 | 114 | empty |
| 2 | 1122 | 0.82 | 0.84 | 109 | empty |
| 3 | 182 | 0.81 | 0.96 | 32 | BTI |
| 4 | 1055 | 0.80 | 0.81 | 94 | ATP |
| 5 | 146 | 0.78 | 0.96 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2683 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2571 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1603 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1520 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1164 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biotinylation).
Compared structures
- 4HNV · Crystal structure of R54E mutant of S. 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 4HNV · PDBe 4HNV · UniProt Q99UY8
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