Research workbench
Crystal structure of the type II dehydroquinate dehydratase from acinetobacter baumannii at 2.03A resolution
Analyse Crystal structure of the type II dehydroquinate dehydratase from acinetobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RC9
- Type
- protein
- Length
- 1,812 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, 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 | 151 | 48% helix, 16% 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.83 | 40 | SO4 |
| 2 | 260 | 0.71 | 0.86 | 32 | SO4 |
| 3 | 573 | 0.70 | 0.79 | 43 | SO4 |
| 4 | 413 | 0.69 | 0.81 | 33 | SO4 |
| 5 | 179 | 0.68 | 0.86 | 34 | empty |
Interfaces
18 interfaces between chains.
- A–D · 972 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 935 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 869 Ų buried · 12 hydrogen bonds · protein-protein
- I–L · 858 Ų buried · 13 hydrogen bonds · protein-protein
- B–K · 858 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4RC9 · Crystal Structure of the type II Dehydroquinate dehydratase from Acinetobacter baumannii… · 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 4RC9 · PDBe 4RC9 · UniProt A3M692
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.