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Crystal structure of type II dehydroquinase from streptomyces coelicolor complexed with phosphate ions
Analyse Crystal structure of type II dehydroquinase from streptomyces coelicolor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D0I
- Type
- protein
- Length
- 1,810 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II 3-dehydroquinate hydratase
- EC
- 4.2.1.10
- UniProt
- P15474
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, I, J | Type II 3-dehydroquinate hydratase (EC 4.2.1.10) | protein | 150 | 47% helix, 15% strand | P15474 |
| D, F, G, K, L | Type II 3-dehydroquinate hydratase (EC 4.2.1.10) | protein | 151 | 46% helix, 16% strand | P15474 |
| E | Type II 3-dehydroquinate hydratase (EC 4.2.1.10) | protein | 152 | 46% helix, 16% strand | P15474 |
| H | Type II 3-dehydroquinate hydratase (EC 4.2.1.10) | protein | 153 | 47% helix, 16% strand | P15474 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.75 | 0.96 | 24 | PO4 |
| 2 | 118 | 0.74 | 0.95 | 27 | PO4 |
| 3 | 51 | 0.68 | 0.97 | 20 | PO4 |
| 4 | 56 | 0.68 | 0.96 | 19 | PO4 |
| 5 | 52 | 0.66 | 0.96 | 20 | PO4 |
Interfaces
18 interfaces between chains.
- E–L · 835 Ų buried · 24 hydrogen bonds · protein-protein
- B–G · 832 Ų buried · 26 hydrogen bonds · protein-protein
- C–J · 831 Ų buried · 23 hydrogen bonds · protein-protein
- F–H · 830 Ų buried · 25 hydrogen bonds · protein-protein
- I–K · 830 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1D0I · Crystal structure of type II dehydroquinase from streptomyces coelicolor complexed with… · the same entry in another collection · chain L against L, 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 P15474
- Elsewhere: RCSB PDB 1D0I · PDBe 1D0I · UniProt P15474
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