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Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with methylmalonyl-coenzyme a and methylmalonic acid bound)
Analyse Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ON3
- Type
- protein
- Length
- 3,093 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, DXX, CD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 517 | 45% helix, 19% strand | Q8GBW6 |
| B | 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 | 510 | 45% helix, 19% strand | Q8GBW6 |
| D | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 513 | 43% helix, 19% strand | Q8GBW6 |
| E | Methylmalonyl-CoA carboxyltransferase 12S subunit (EC 2.1.3.1) | protein | 520 | 45% helix, 19% strand | Q8GBW6 |
Ligands and binding sites
- MCA · Methylmalonyl-coenzyme A · ligand · 6 copies · chains A, D, B, E, C, F
- DXX · Methylmalonic acid · ligand · 6 copies · chains A, D, B, E, C, F
- CD · Cadmium ion · metal · 3 copies · chains A, D, B, E, C, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, 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 | 865 | 0.81 | 0.84 | 84 | empty |
| 2 | 734 | 0.81 | 0.85 | 111 | empty |
| 3 | 1152 | 0.80 | 0.82 | 104 | empty |
| 4 | 60 | 0.73 | 0.99 | 27 | empty |
| 5 | 567 | 0.69 | 0.78 | 57 | MCA, DXX |
Interfaces
12 interfaces between chains.
- A–D · 4854 Ų buried · 64 hydrogen bonds · protein-protein
- B–E · 4839 Ų buried · 63 hydrogen bonds · protein-protein
- C–F · 4794 Ų buried · 67 hydrogen bonds · protein-protein
- E–F · 1477 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1395 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1ON3 · 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 1ON3 · PDBe 1ON3 · UniProt Q8GBW6
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