MolNFT v1 · #16678 · protein
Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase
1O66: “Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase”. X-ray diffraction, 14 pockets (best druggability 0.63). MolNFT v1 #16678 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1O66
- Type
- protein
- Length
- 1,229 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methyl-2-oxobutanoate hydroxymethyltransferase
- EC
- 2.1.2.11
- UniProt
- Q9JZW6
- Pockets
- 14 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 249 | 44% helix, 15% strand | Q9JZW6 |
| B | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 248 | 44% helix, 15% strand | Q9JZW6 |
| C | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 246 | 43% helix, 15% strand | Q9JZW6 |
| D | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 249 | 43% helix, 15% strand | Q9JZW6 |
| E | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 237 | 43% helix, 16% strand | Q9JZW6 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.63 | 0.82 | 30 | empty |
| 2 | 216 | 0.61 | 0.81 | 30 | empty |
| 3 | 260 | 0.61 | 0.80 | 37 | empty |
| 4 | 207 | 0.60 | 0.81 | 28 | empty |
| 5 | 287 | 0.57 | 0.77 | 40 | empty |
Interfaces
5 interfaces between chains.
- C–D · 639 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 610 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 599 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 435 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 75 modified (engineered).
Compared structures
- 1O66 · Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase · the same entry in another collection · chain E against E, TM-score 1.00
- Q9JZW6 · AlphaFold monomer V2.0 prediction for 3-methyl-2-oxobutanoate hydroxymethyltransferase… · a predicted model of the same protein · chain D 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 Q9JZW6
- Elsewhere: RCSB PDB 1O66 · PDBe 1O66 · UniProt Q9JZW6
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