Research workbench
Crystal structure of human pyruvate carboxylase (missing the biotin carboxylase domain at the N-terminus)
Analyse Crystal structure of human pyruvate carboxylase (missing the biotin carboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BG3
- Type
- protein
- Length
- 2,568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase, mitochondrial
- EC
- 6.4.1.1
- UniProt
- P11498
- Ligands
- PYR, BTI, MN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyruvate carboxylase, mitochondrial (EC 6.4.1.1) | protein | 680 | 42% helix, 15% strand | P11498 |
| B, C | Pyruvate carboxylase, mitochondrial (EC 6.4.1.1) | protein | 604 | 44% helix, 12% strand | P11498 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · chains A, B
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.83 | 0.93 | 44 | BTI, PYR |
| 2 | 158 | 0.82 | 0.98 | 38 | empty |
| 3 | 161 | 0.82 | 0.98 | 39 | empty |
| 4 | 1086 | 0.80 | 0.82 | 109 | empty |
| 5 | 863 | 0.78 | 0.81 | 92 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1604 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1492 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 793 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 503 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 399 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 cofactor (carboxylation, biotinylation).
Compared structures
- 3BG3 · Crystal Structure of Human Pyruvate Carboxylase (missing the biotin carboxylase domain at… · the same entry in another collection · chain A against A, TM-score 1.00
- P11498 · AlphaFold monomer V2.0 prediction for pyruvate carboxylase, mitochondrial (P11498) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P11498
- Elsewhere: RCSB PDB 3BG3 · PDBe 3BG3 · UniProt P11498
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