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Structure of the carboxyl transferase domain from rhizobium etli pyruvate carboxylase with pyruvate and biocytin
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
- 4M6V
- Type
- protein
- Length
- 2,379 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
- BYT, PYR, ZN, MG, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate carboxylase (EC 6.4.1.1) | protein | 597 | 48% helix, 12% strand | Q2K340 |
| B | Pyruvate carboxylase (EC 6.4.1.1) | protein | 593 | 49% helix, 13% strand | Q2K340 |
| C | Pyruvate carboxylase (EC 6.4.1.1) | protein | 596 | 48% helix, 13% strand | Q2K340 |
| D | Pyruvate carboxylase (EC 6.4.1.1) | protein | 593 | 49% helix, 13% strand | Q2K340 |
Ligands and binding sites
- BYT · Biocytin · ligand · 8 copies · chains A, B, C, D
- PYR · Pyruvic acid · 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, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.80 | 0.85 | 93 | PYR, BYT |
| 2 | 606 | 0.79 | 0.85 | 85 | PYR, BYT |
| 3 | 556 | 0.78 | 0.85 | 86 | PYR, BYT |
| 4 | 542 | 0.77 | 0.84 | 75 | BYT |
| 5 | 500 | 0.67 | 0.78 | 52 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1503 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1493 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 339 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 4M6V · 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 4M6V · PDBe 4M6V · UniProt Q2K340
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