MolNFT v1 · #14262 · protein
Crystal structure of ketopantoate hydroxymethyltransferase complexed the product ketopantoate
1M3U · 3-methyl-2-oxobutanoate hydroxymethyltransferase: “Crystal structure of ketopantoate hydroxymethyltransferase complexed the product ketopantoate”. X-ray diffraction, 2 ligands (KPL, MG), 20 pockets (best druggability 0.77). MolNFT…
- PDB
- 1M3U
- Type
- protein
- Length
- 2,620 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methyl-2-oxobutanoate hydroxymethyltransferase
- EC
- 2.1.2.11
- UniProt
- P31057
- Ligands
- KPL, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 262 | 45% helix, 14% strand | P31057 |
Ligands and binding sites
- KPL · Ketopantoate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.77 | 0.79 | 104 | MG, KPL |
| 2 | 364 | 0.70 | 0.82 | 47 | MG, KPL |
| 3 | 606 | 0.69 | 0.78 | 69 | empty |
| 4 | 372 | 0.69 | 0.81 | 43 | MG, KPL |
| 5 | 627 | 0.69 | 0.78 | 64 | empty |
Interfaces
15 interfaces between chains.
- A–F · 1181 Ų buried · 21 hydrogen bonds · protein-protein
- E–J · 1168 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 1149 Ų buried · 22 hydrogen bonds · protein-protein
- C–H · 1111 Ų buried · 16 hydrogen bonds · protein-protein
- D–I · 1103 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1M3U · Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product… · the same entry in another collection · chain J against J, TM-score 1.00
- P31057 · AlphaFold monomer V2.0 prediction for 3-methyl-2-oxobutanoate hydroxymethyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31057
- Elsewhere: RCSB PDB 1M3U · PDBe 1M3U · UniProt P31057
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.