MolNFT v1 · #17245 · protein
Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with hydrolyzed methylmalonyl-coenzyme a bound)
1ON9 · Methylmalonyl-CoA carboxyltransferase 12S subunit: “Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with…”. X-ray diffraction, 2 ligands (MCA, CD), 20 pockets (best druggability…
- PDB
- 1ON9
- Type
- protein
- Length
- 3,085 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA carboxyltransferase 12S subunit
- EC
- 2.1.3.1
- UniProt
- Q8GBW6
- Ligands
- MCA, CD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 516 | 46% helix, 19% strand | Q8GBW6 |
| C | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 514 | 45% helix, 19% strand | Q8GBW6 |
| D | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 504 | 45% helix, 19% strand | Q8GBW6 |
| E | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 519 | 46% helix, 19% strand | Q8GBW6 |
Ligands and binding sites
- MCA · Methylmalonyl-coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
- CD · Cadmium ion · metal · 3 copies · chains A, D, B, E, C, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.82 | 0.84 | 92 | empty |
| 2 | 813 | 0.81 | 0.84 | 90 | empty |
| 3 | 710 | 0.80 | 0.85 | 97 | empty |
| 4 | 471 | 0.67 | 0.78 | 44 | empty |
| 5 | 468 | 0.66 | 0.78 | 51 | empty |
Interfaces
14 interfaces between chains.
- B–E · 4813 Ų buried · 76 hydrogen bonds · protein-protein
- A–D · 4808 Ų buried · 70 hydrogen bonds · protein-protein
- C–F · 4767 Ų buried · 68 hydrogen bonds · protein-protein
- D–F · 1421 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1367 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1ON9 · Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8GBW6 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA carboxyltransferase 12S subunit… · a predicted model of the same protein · chain B 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 Q8GBW6
- Elsewhere: RCSB PDB 1ON9 · PDBe 1ON9 · UniProt Q8GBW6
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