MolNFT v1 · #63095 · protein
Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from burkholderia pseudomallei
3EZ4: “Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from burkholderia pseudomallei”. X-ray diffraction, 16 pockets (best druggability 0.74). MolNFT v1 #63095 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3EZ4
- Type
- protein
- Length
- 2,433 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
- Q63R49
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 9 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 | 242 | 44% helix, 15% strand | Q63R49 |
| B | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 242 | 43% helix, 16% strand | Q63R49 |
| C | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 243 | 43% helix, 16% strand | Q63R49 |
| D | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 242 | 43% helix, 15% strand | Q63R49 |
| E, J | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 243 | 44% helix, 15% strand | Q63R49 |
| F | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 246 | 44% helix, 15% strand | Q63R49 |
| G | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 241 | 43% helix, 16% strand | Q63R49 |
| H | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 245 | 44% helix, 16% strand | Q63R49 |
| I | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 246 | 43% helix, 15% strand | Q63R49 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains E, J, A, F, B, G, C, H, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.74 | 0.78 | 104 | empty |
| 2 | 1110 | 0.71 | 0.75 | 112 | empty |
| 3 | 973 | 0.71 | 0.75 | 108 | empty |
| 4 | 980 | 0.71 | 0.75 | 106 | empty |
| 5 | 657 | 0.64 | 0.74 | 55 | empty |
Interfaces
15 interfaces between chains.
- B–G · 1209 Ų buried · 16 hydrogen bonds · protein-protein
- E–J · 1138 Ų buried · 15 hydrogen bonds · protein-protein
- D–I · 1120 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1118 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 1108 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3EZ4 · Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia… · the same entry in another collection · chain J against J, TM-score 1.00
- Q63R49 · AlphaFold monomer V2.0 prediction for 3-methyl-2-oxobutanoate hydroxymethyltransferase… · 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 Q63R49
- Elsewhere: RCSB PDB 3EZ4 · PDBe 3EZ4 · UniProt Q63R49
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