Research workbench
Structure of rhizobium etli pyruvate carboxylase T882A with the allosteric activator, acetyl coenzyme-a
Analyse Structure of rhizobium etli pyruvate carboxylase T882A with the allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TW6
- Type
- protein
- Length
- 4,309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase protein
- EC
- 6.4.1.1
- UniProt
- Q2K340
- Ligands
- ADP, COA, BTI, PAE, MG, ZN, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase protein (EC 6.4.1.1) | protein | 1007 | 40% helix, 18% strand | Q2K340 |
| B | Pyruvate carboxylase protein (EC 6.4.1.1) | protein | 1129 | 40% helix, 19% strand | Q2K340 |
| C | Pyruvate carboxylase protein (EC 6.4.1.1) | protein | 1044 | 42% helix, 18% strand | Q2K340 |
| D | Pyruvate carboxylase protein (EC 6.4.1.1) | protein | 1129 | 38% helix, 17% strand | Q2K340 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- COA · Coenzyme A · ligand · 2 copies · chains A, C
- BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · chains B
- PAE · Phosphonoacetic acid · ligand · chains C
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 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 | 767 | 0.81 | 0.84 | 116 | empty |
| 2 | 1084 | 0.81 | 0.82 | 126 | empty |
| 3 | 1097 | 0.79 | 0.81 | 83 | ADP, MG, BTI |
| 4 | 995 | 0.77 | 0.79 | 117 | ADP, MG |
| 5 | 837 | 0.74 | 0.79 | 80 | ADP, MG, PAE |
Interfaces
3 interfaces between chains.
- C–D · 1604 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1498 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 434 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 3TW6 · Structure of Rhizobium etli pyruvate carboxylase T882A with the allosteric activator… · 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 Q2K340
- Elsewhere: RCSB PDB 3TW6 · PDBe 3TW6 · UniProt Q2K340
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