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Structure of the carboxyl transferase domain from rhizobium etli pyruvate carboxylase with oxalate
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
- 4MFD
- Type
- protein
- Length
- 2,387 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
- OXL, ZN, MG, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 597 | 48% helix, 13% strand | Q2K340 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 596 | 48% helix, 13% strand | Q2K340 |
Ligands and binding sites
- OXL · Oxalate ion · 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 · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C, B, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.75 | 0.88 | 39 | empty |
| 2 | 353 | 0.73 | 0.85 | 44 | empty |
| 3 | 261 | 0.73 | 0.87 | 36 | empty |
| 4 | 402 | 0.72 | 0.83 | 59 | OXL |
| 5 | 284 | 0.72 | 0.85 | 41 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1549 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1469 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 354 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 303 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 4MFD · Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase… · the same entry in another collection · chain C against C, 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 4MFD · PDBe 4MFD · UniProt Q2K340
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