MolNFT v1 · #58860 · protein
Crystal structure of human pyruvate carboxylase (missing the biotin carboxylase domain at the N-terminus) F1077A mutant
3BG9 · Pyruvate carboxylase, mitochondrial: “Crystal structure of human pyruvate carboxylase (missing the biotin carboxylase domain at the N-terminus)…”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3BG9
- Type
- protein
- Length
- 2,404 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
- MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate carboxylase, mitochondrial (EC 6.4.1.1) | protein | 601 | 47% helix, 10% strand | P11498 |
Ligands and binding sites
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.81 | 0.97 | 35 | empty |
| 2 | 159 | 0.80 | 0.97 | 34 | empty |
| 3 | 832 | 0.78 | 0.82 | 102 | empty |
| 4 | 704 | 0.74 | 0.80 | 79 | empty |
| 5 | 708 | 0.74 | 0.80 | 79 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1666 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1665 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 389 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3BG9 · 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 A 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 3BG9 · PDBe 3BG9 · UniProt P11498
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