Research workbench
Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from burkholderia thailandensis
Analyse Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VAV
- Type
- protein
- Length
- 2,536 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
- Q2SYZ1
- Ligands
- CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 9 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 260 | 45% helix, 15% strand | Q2SYZ1 |
| B | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 260 | 44% helix, 15% strand | Q2SYZ1 |
| C | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 243 | 43% helix, 14% strand | Q2SYZ1 |
| D | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 259 | 43% helix, 14% strand | Q2SYZ1 |
| E | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 251 | 43% helix, 15% strand | Q2SYZ1 |
| F | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 253 | 45% helix, 15% strand | Q2SYZ1 |
| G | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 239 | 44% helix, 15% strand | Q2SYZ1 |
| H, J | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 263 | 44% helix, 14% strand | Q2SYZ1 |
| I | 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 245 | 44% helix, 15% strand | Q2SYZ1 |
Ligands and binding sites
- CL · Chloride ion · ion · chains D, I
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, F, B, G, C, D, I, E, H, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.72 | 0.76 | 109 | EDO |
| 2 | 994 | 0.72 | 0.75 | 99 | EDO |
| 3 | 815 | 0.70 | 0.76 | 94 | EDO |
| 4 | 742 | 0.70 | 0.77 | 74 | EDO |
| 5 | 772 | 0.69 | 0.76 | 70 | empty |
Interfaces
15 interfaces between chains.
- C–H · 1197 Ų buried · 16 hydrogen bonds · protein-protein
- E–J · 1169 Ų buried · 15 hydrogen bonds · protein-protein
- D–I · 1163 Ų buried · 14 hydrogen bonds · protein-protein
- B–G · 1140 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1134 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3VAV · Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia… · the same entry in another collection · chain J against J, TM-score 1.00
- Q2SYZ1 · AlphaFold monomer V2.0 prediction for 3-methyl-2-oxobutanoate hydroxymethyltransferase… · a predicted model of the same protein · chain F 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 Q2SYZ1
- Elsewhere: RCSB PDB 3VAV · PDBe 3VAV · UniProt Q2SYZ1
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