MolNFT v1 · #32527 · protein
Type II dehydroquinase inhibitor complex
2BT4 · 3-dehydroquinate dehydratase: “Type II dehydroquinase inhibitor complex”. X-ray diffraction, 2 ligands (CA2, PO4), 20 pockets (best druggability 0.81). MolNFT v1 #32527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BT4
- Type
- protein
- Length
- 1,788 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P15474
- Ligands
- CA2, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 149 | 47% helix, 16% strand | P15474 |
Ligands and binding sites
- CA2 · (1S,3R,4R,5S)-1,3,4-trihydroxy-5-(3-phenoxypropyl)cyclohexanecarboxylic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 12 copies · chains A, D, B, G, C, J, E, L, F, H, I, K
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.81 | 0.95 | 25 | CA2 |
| 2 | 164 | 0.79 | 0.95 | 25 | CA2 |
| 3 | 168 | 0.78 | 0.94 | 24 | CA2 |
| 4 | 171 | 0.78 | 0.94 | 25 | CA2 |
| 5 | 174 | 0.78 | 0.94 | 26 | CA2 |
Interfaces
18 interfaces between chains.
- A–D · 861 Ų buried · 28 hydrogen bonds · protein-protein
- B–G · 858 Ų buried · 30 hydrogen bonds · protein-protein
- I–K · 857 Ų buried · 27 hydrogen bonds · protein-protein
- C–J · 857 Ų buried · 26 hydrogen bonds · protein-protein
- E–L · 849 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2BT4 · Type II Dehydroquinase inhibitor complex · the same entry in another collection · chain I against I, 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 2BT4 · PDBe 2BT4 · UniProt P15474
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