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Crystal structure of putative dehydratase protein from salmonella enterica subsp. enterica serovar typhimurium (salmonella typhimurium)
Analyse Crystal structure of putative dehydratase protein from salmonella enterica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E6M
- Type
- protein
- Length
- 3,208 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydratase protein
- UniProt
- Q8ZNH1
- Ligands
- MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative dehydratase protein | protein | 401 | 42% helix, 17% strand | Q8ZNH1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B, F, C, D, E, G, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 8 copies · chains B, A, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.89 | 0.97 | 38 | empty |
| 2 | 428 | 0.88 | 0.96 | 37 | empty |
| 3 | 429 | 0.88 | 0.96 | 39 | empty |
| 4 | 399 | 0.87 | 0.96 | 39 | empty |
| 5 | 1123 | 0.83 | 0.84 | 117 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2463 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2462 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2455 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2452 Ų buried · 35 hydrogen bonds · protein-protein
- C–H · 1477 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4E6M · Crystal structure of Putative dehydratase protein from Salmonella enterica subsp.… · the same entry in another collection · chain A 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 Q8ZNH1
- Elsewhere: RCSB PDB 4E6M · PDBe 4E6M · UniProt Q8ZNH1
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