Research workbench
Crystal structure of 2-methylcitrate synthase from aspergillus fumigatus
Analyse Crystal structure of 2-methylcitrate synthase from aspergillus fumigatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UQQ
- Type
- protein
- Length
- 2,611 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-methylcitrate synthase, mitochondrial
- EC
- 2.3.3.5, 2.3.3.16
- UniProt
- Q50I20
- Ligands
- SRT
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 2-methylcitrate synthase, mitochondrial (EC 2.3.3.5, 2.3.3.16) | protein | 436 | 64% helix, 6% strand | Q50I20 |
| C | 2-methylcitrate synthase, mitochondrial (EC 2.3.3.5, 2.3.3.16) | protein | 437 | 63% helix, 6% strand | Q50I20 |
| A, F | 2-methylcitrate synthase, mitochondrial (EC 2.3.3.5, 2.3.3.16) | protein | 435 | 64% helix, 6% strand | Q50I20 |
| D, E | 2-methylcitrate synthase, mitochondrial (EC 2.3.3.5, 2.3.3.16) | protein | 434 | 63% helix, 6% strand | Q50I20 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.80 | 0.83 | 93 | empty |
| 2 | 807 | 0.73 | 0.78 | 103 | empty |
| 3 | 624 | 0.71 | 0.79 | 75 | empty |
| 4 | 530 | 0.70 | 0.79 | 56 | empty |
| 5 | 534 | 0.69 | 0.79 | 58 | SRT |
Interfaces
10 interfaces between chains.
- E–F · 4402 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 4321 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 4315 Ų buried · 48 hydrogen bonds · protein-protein
- C–E · 438 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 270 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5UQQ · Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus · the same entry in another collection · chain F against F, TM-score 1.00
- Q50I20 · AlphaFold monomer V2.0 prediction for 2-methylcitrate synthase, mitochondrial (Q50I20) · 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 Q50I20
- Elsewhere: RCSB PDB 5UQQ · PDBe 5UQQ · UniProt Q50I20
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