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Structure of the carboxyl transferase domain from rhizobium etli pyruvate carboxylase with 3-hydroxypyruvate
Analyse Structure of the carboxyl transferase domain from rhizobium etli pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MFE
- Type
- protein
- Length
- 2,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate carboxylase
- EC
- 6.4.1.1
- UniProt
- Q2K340
- Ligands
- 3PY, BTN, ZN, MG, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 597 | 48% helix, 12% strand | Q2K340 |
| B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 594 | 49% helix, 13% strand | Q2K340 |
| D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 594 | 48% helix, 12% strand | Q2K340 |
Ligands and binding sites
- 3PY · 3-hydroxypyruvic acid · ligand · 4 copies · chains A, B, C, D
- BTN · Biotin · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.78 | 0.81 | 110 | empty |
| 2 | 685 | 0.78 | 0.83 | 100 | 3PY |
| 3 | 668 | 0.78 | 0.83 | 99 | 3PY |
| 4 | 299 | 0.68 | 0.83 | 43 | empty |
| 5 | 302 | 0.65 | 0.81 | 43 | 3PY |
Interfaces
4 interfaces between chains.
- C–D · 1437 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1381 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 286 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 4MFE · Structure of the carboxyl transferase domain from Rhizobium etli 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 Q2K340
- Elsewhere: RCSB PDB 4MFE · PDBe 4MFE · UniProt Q2K340
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