Research workbench
Crystal structure of two-subunit pyruvate carboxylase from methylobacillus flagellatus
Analyse Crystal structure of two-subunit pyruvate carboxylase from methylobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KS8
- Type
- protein
- Length
- 2,903 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase subunit alpha; Pyruvate carboxylase subunit beta
- UniProt
- Q1H158, Q1H157
- Ligands
- PYR, BTI, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate carboxylase subunit alpha | protein | 404 | 37% helix, 24% strand | Q1H158 |
| C | Pyruvate carboxylase subunit beta | protein | 603 | 38% helix, 18% strand | Q1H157 |
| D | Pyruvate carboxylase subunit beta | protein | 580 | 39% helix, 17% strand | Q1H157 |
| E | Pyruvate carboxylase subunit beta | protein | 430 | 45% helix, 16% strand | Q1H157 |
| F | Pyruvate carboxylase subunit beta | protein | 482 | 36% helix, 21% strand | Q1H157 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains C, D
- BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · chains C, D
- MN · Manganese (II) ion · metal · 3 copies · chains C, D, F
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 | 348 | 0.85 | 0.94 | 67 | empty |
| 2 | 995 | 0.84 | 0.85 | 120 | empty |
| 3 | 1051 | 0.81 | 0.82 | 100 | PYR |
| 4 | 140 | 0.79 | 0.97 | 29 | empty |
| 5 | 121 | 0.79 | 0.97 | 31 | BTI, PYR |
Interfaces
11 interfaces between chains.
- C–D · 3886 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1625 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1503 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 845 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 821 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (biotinylation).
Compared structures
- 5KS8 · Crystal structure of two-subunit pyruvate carboxylase from Methylobacillus flagellatus · 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 Q1H158
- Every structure of UniProt Q1H157
- Elsewhere: RCSB PDB 5KS8 · PDBe 5KS8 · UniProt Q1H158 · UniProt Q1H157
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