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1.95 ångström crystal structure of of type I 3-dehydroquinate dehydratase (arod) from clostridium difficile with covalent modified comenic acid.
Analyse 1.95 ångström crystal structure of of type I 3-dehydroquinate dehydratase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H3D
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- Q186A6
- Ligands
- SHL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 252 | 46% helix, 20% strand | Q186A6 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 254 | 46% helix, 20% strand | Q186A6 |
| D | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 253 | 46% helix, 20% strand | Q186A6 |
Ligands and binding sites
- SHL · 5-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains B, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.83 | 0.89 | 49 | empty |
| 2 | 508 | 0.82 | 0.88 | 53 | empty |
| 3 | 635 | 0.81 | 0.86 | 70 | empty |
| 4 | 323 | 0.63 | 0.79 | 32 | SHL |
| 5 | 229 | 0.61 | 0.81 | 27 | SHL |
Interfaces
6 interfaces between chains.
- C–D · 1242 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1239 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 587 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 4H3D · 1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q186A6 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q186A6) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q186A6
- Elsewhere: RCSB PDB 4H3D · PDBe 4H3D · UniProt Q186A6
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