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Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815
Analyse Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CV6
- Type
- protein
- Length
- 1,737 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Paraburkholderia phymatum
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- B2JVW0
- Ligands
- CL
- Pockets
- 19 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.6 · 4 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, H | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 145 | 50% helix, 18% strand | B2JVW0 |
| B, C, E | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 145 | 50% helix, 19% strand | B2JVW0 |
| D, J, K, L | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 144 | 49% helix, 18% strand | B2JVW0 |
| I | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 146 | 49% helix, 19% strand | B2JVW0 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B, G
- TLA · L(+)-tartaric acid · additive · 24 copies · chains A, B, E, C, D, F, G, I, H, J, K, L
- TAR · D(-)-tartaric acid · additive · 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
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.66 | 0.83 | 25 | TLA |
| 2 | 275 | 0.65 | 0.82 | 28 | TLA |
| 3 | 284 | 0.65 | 0.82 | 25 | TLA |
| 4 | 273 | 0.65 | 0.82 | 26 | TLA |
| 5 | 278 | 0.65 | 0.82 | 27 | TLA |
Interfaces
16 interfaces between chains.
- A–B · 702 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 700 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 698 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 698 Ų buried · 11 hydrogen bonds · protein-protein
- G–I · 698 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6CV6 · Crystal structure of 3-dehydroquinate dehydratase, type II, from burkholderia phymatum… · the same entry in another collection · chain A against A, 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 B2JVW0
- Elsewhere: RCSB PDB 6CV6 · PDBe 6CV6 · UniProt B2JVW0
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