MolNFT v1 · #127401 · protein
Crystal structure of 2-methylcitrate dehydratase (prpd) from salmonella enterica
5MVI: “Crystal structure of 2-methylcitrate dehydratase (prpd) from salmonella enterica”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #127401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MVI
- Type
- protein
- Length
- 2,134 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-methylcitrate dehydratase
- EC
- 4.2.1.79
- UniProt
- A0A0L5RC52
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, B, F | 2-methylcitrate dehydratase (EC 4.2.1.79) | protein | 334 | 57% helix, 4% strand | A0A0L5RC52 |
| D | 2-methylcitrate dehydratase (EC 4.2.1.79) | protein | 337 | 56% helix, 4% strand | A0A0L5RC52 |
| A | 2-methylcitrate dehydratase (EC 4.2.1.79) | protein | 463 | 52% helix, 8% strand | A0A0L5RC52 |
| C | 2-methylcitrate dehydratase (EC 4.2.1.79) | protein | 332 | 57% helix, 5% strand | A0A0L5RC52 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.86 | 0.89 | 93 | empty |
| 2 | 538 | 0.86 | 0.91 | 84 | empty |
| 3 | 568 | 0.85 | 0.91 | 87 | empty |
| 4 | 151 | 0.79 | 0.95 | 32 | empty |
| 5 | 644 | 0.75 | 0.81 | 71 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2286 Ų buried · 27 hydrogen bonds · protein-protein
- D–C · 2225 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2155 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 273 Ų buried · 2 hydrogen bonds · protein-protein
- D–A · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MVI · Crystal structure of 2-methylcitrate dehydratase (PrpD) from Salmonella enterica · the same entry in another collection · chain E against E, 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 A0A0L5RC52
- Elsewhere: RCSB PDB 5MVI · PDBe 5MVI · UniProt A0A0L5RC52
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