Research workbench
Structure of the dodecameric type-II dehydrogenate dehydratase from acinetobacter baumannii at 2.00 a resolution
Analyse Structure of the dodecameric type-II dehydrogenate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B6P
- Type
- protein
- Length
- 1,740 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
- A3M692
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% 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 | 145 | 48% helix, 17% strand | A3M692 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.72 | 0.83 | 36 | SO4 |
| 2 | 405 | 0.71 | 0.82 | 30 | SO4 |
| 3 | 397 | 0.70 | 0.82 | 33 | SO4 |
| 4 | 390 | 0.70 | 0.82 | 29 | SO4 |
| 5 | 398 | 0.69 | 0.81 | 29 | SO4 |
Interfaces
18 interfaces between chains.
- E–H · 874 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 865 Ų buried · 14 hydrogen bonds · protein-protein
- I–L · 864 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 863 Ų buried · 14 hydrogen bonds · protein-protein
- B–K · 860 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5B6P · Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter… · 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 A3M692
- Elsewhere: RCSB PDB 5B6P · PDBe 5B6P · UniProt A3M692
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