Research workbench
Crystal structure of F403A mutant of S. aureus pyruvate carboxylase
Analyse Crystal structure of F403A 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
- 4HNT
- Type
- protein
- Length
- 4,089 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
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1052 | 39% helix, 17% strand | Q99UY8 |
| B, D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 989 | 43% helix, 18% strand | Q99UY8 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 1059 | 39% helix, 18% strand | Q99UY8 |
Ligands and binding sites
- BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · 3 copies · chains A, B, 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
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 | 1107 | 0.84 | 0.84 | 105 | empty |
| 2 | 1181 | 0.83 | 0.84 | 107 | empty |
| 3 | 960 | 0.82 | 0.83 | 78 | ATP |
| 4 | 188 | 0.81 | 0.96 | 34 | empty |
| 5 | 147 | 0.80 | 0.97 | 33 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2636 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2620 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 1498 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1479 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4HNT · crystal structure of F403A 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 4HNT · PDBe 4HNT · UniProt Q99UY8
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