MolNFT v1 · #99555 · protein
Structure of the carboxyl transferase domain from rhizobium etli pyruvate carboxylase with pyruvate and biocytin
4M6V: “Structure of the carboxyl transferase domain from rhizobium etli pyruvate carboxylase with pyruvate and…”. X-ray diffraction, 5 ligands (BYT, PYR, ZN), 20 pockets (best druggability 0.80). MolNFT v1 #99555 on GenesisL1: 3D…
- 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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