MolNFT v1 · #47390 · protein
Crystal structure of putative dehydratase from zymomonas mobilis ZM4
2OX4 · Putative mandelate racemase: “Crystal structure of putative dehydratase from zymomonas mobilis ZM4”. X-ray diffraction, 2 ligands (MG, CL), 20 pockets (best druggability 0.87). MolNFT v1 #47390 on GenesisL1: 3D structure, binding…
- PDB
- 2OX4
- Type
- protein
- Length
- 3,152 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mandelate racemase
- EC
- 5.1.2.2
- UniProt
- Q5NN22
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H | Putative mandelate racemase (EC 5.1.2.2) | protein | 393 | 41% helix, 17% strand | Q5NN22 |
| C, D | Putative mandelate racemase (EC 5.1.2.2) | protein | 397 | 41% helix, 18% strand | Q5NN22 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E, F, H, C, G
- GOL · Glycerol · additive · 14 copies · chains A, B, H, C, G, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.87 | 0.88 | 93 | empty |
| 2 | 478 | 0.82 | 0.89 | 41 | empty |
| 3 | 539 | 0.82 | 0.88 | 51 | empty |
| 4 | 1190 | 0.82 | 0.83 | 123 | empty |
| 5 | 994 | 0.79 | 0.80 | 98 | empty |
Interfaces
16 interfaces between chains.
- F–H · 2015 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1984 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 1982 Ų buried · 31 hydrogen bonds · protein-protein
- C–G · 1979 Ų buried · 33 hydrogen bonds · protein-protein
- A–H · 1344 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2OX4 · Crystal structure of putative dehydratase from Zymomonas mobilis ZM4 · 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 Q5NN22
- Elsewhere: RCSB PDB 2OX4 · PDBe 2OX4 · UniProt Q5NN22
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