MolNFT v1 · #164073 · protein
The crystal structure of type II dehydroquinase from zymomonas mobilis
6SMF · 3-dehydroquinate dehydratase: “The crystal structure of type II dehydroquinase from zymomonas mobilis”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.71). MolNFT v1 #164073 on GenesisL1: 3D structure, binding…
- PDB
- 6SMF
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- Q5NPJ9
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 144 | 50% helix, 18% strand | Q5NPJ9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.99 | 28 | empty |
| 2 | 242 | 0.66 | 0.84 | 25 | FLC |
| 3 | 343 | 0.64 | 0.80 | 28 | FLC |
| 4 | 260 | 0.62 | 0.80 | 25 | FLC |
| 5 | 145 | 0.49 | 0.78 | 25 | TRS |
Interfaces
4 interfaces between chains.
- A–D · 882 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 739 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 724 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6SMF · The crystal structure of type II dehydroquinase from zymomonas mobilis · 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 Q5NPJ9
- Elsewhere: RCSB PDB 6SMF · PDBe 6SMF · UniProt Q5NPJ9
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