Research workbench
H.PYLORI type II dehydroquinase in complex with FA1
Analyse H.PYLORI type II dehydroquinase in complex with FA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C57
- Type
- protein
- Length
- 1,880 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
- Q48255
- Ligands
- FA1
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 164 | 46% helix, 20% strand | Q48255 |
| B, C, E, F, H, I, K, L | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 153 | 51% helix, 18% strand | Q48255 |
Ligands and binding sites
- FA1 · 2,3 -anhydro-quinic acid · ligand · 12 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 | 202 | 0.66 | 0.84 | 22 | FA1 |
| 2 | 196 | 0.63 | 0.83 | 28 | FA1 |
| 3 | 226 | 0.62 | 0.82 | 26 | FA1 |
| 4 | 220 | 0.62 | 0.82 | 25 | FA1 |
| 5 | 218 | 0.61 | 0.82 | 27 | FA1 |
Interfaces
18 interfaces between chains.
- A–G · 961 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 958 Ų buried · 14 hydrogen bonds · protein-protein
- D–J · 955 Ų buried · 17 hydrogen bonds · protein-protein
- I–L · 954 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 944 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2C57 · H.pylori type II dehydroquinase in complex with FA1 · 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 Q48255
- Elsewhere: RCSB PDB 2C57 · PDBe 2C57 · UniProt Q48255
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