MolNFT v1 · #144276 · protein
Crystal structure of 2-methylcitrate synthase from aspergillus fumigatus with oxaloacetate and coenzyme-a.
6BOO · 2-methylcitrate synthase, mitochondrial: “Crystal structure of 2-methylcitrate synthase from aspergillus fumigatus with oxaloacetate and coenzyme-a.”. X-ray diffraction, 2 ligands (OAA, COA), 12 pockets (best druggability 0.78).…
- PDB
- 6BOO
- Type
- protein
- Length
- 1,740 residues
- Chains
- 4
- 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
- B0YD89
- Ligands
- OAA, COA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | 2-methylcitrate synthase, mitochondrial (EC 2.3.3.5, 2.3.3.16) | protein | 435 | 63% helix, 6% strand | B0YD89 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 5 copies · chains B, C, A, D
- COA · Coenzyme A · ligand · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.78 | 0.83 | 80 | empty |
| 2 | 442 | 0.78 | 0.86 | 53 | OAA, COA |
| 3 | 930 | 0.76 | 0.79 | 78 | OAA |
| 4 | 642 | 0.75 | 0.81 | 55 | OAA, COA |
| 5 | 794 | 0.73 | 0.78 | 61 | OAA |
Interfaces
6 interfaces between chains.
- B–C · 4772 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 4766 Ų buried · 65 hydrogen bonds · protein-protein
- B–D · 602 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
- B–A · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BOO · Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus with… · the same entry in another collection · chain A against A, TM-score 1.00
- B0YD89 · AlphaFold monomer V2.0 prediction for 2-methylcitrate synthase, mitochondrial (B0YD89) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B0YD89
- Elsewhere: RCSB PDB 6BOO · PDBe 6BOO · UniProt B0YD89
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