MolNFT v1 · #127381 · protein
Crystal structure of 2-methylcitrate dehydratase (mmge) from bacillus subtilis.
5MUX: “Crystal structure of 2-methylcitrate dehydratase (mmge) from bacillus subtilis.”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #127381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MUX
- Type
- protein
- Length
- 2,824 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-methylcitrate dehydratase
- EC
- 4.2.1.79, 4.2.1.3
- UniProt
- P45859
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-methylcitrate dehydratase (EC 4.2.1.79, 4.2.1.3) | protein | 469 | 55% helix, 8% strand | P45859 |
| B, C, E | 2-methylcitrate dehydratase (EC 4.2.1.79, 4.2.1.3) | protein | 472 | 56% helix, 8% strand | P45859 |
| D | 2-methylcitrate dehydratase (EC 4.2.1.79, 4.2.1.3) | protein | 471 | 56% helix, 8% strand | P45859 |
| F | 2-methylcitrate dehydratase (EC 4.2.1.79, 4.2.1.3) | protein | 468 | 55% helix, 7% strand | P45859 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.86 | 0.89 | 82 | empty |
| 2 | 1186 | 0.85 | 0.85 | 110 | empty |
| 3 | 325 | 0.85 | 0.94 | 52 | empty |
| 4 | 278 | 0.84 | 0.96 | 40 | empty |
| 5 | 1146 | 0.84 | 0.85 | 100 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2483 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2467 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2453 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 513 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 496 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5MUX · Crystal structure of 2-methylcitrate dehydratase (MmgE) from Bacillus subtilis. · the same entry in another collection · chain F against F, TM-score 1.00
- P45859 · AlphaFold monomer V2.0 prediction for CITRATE/2-methylcitrate dehydratase (P45859) · a predicted model of the same protein · chain D 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 P45859
- Elsewhere: RCSB PDB 5MUX · PDBe 5MUX · UniProt P45859
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