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Crystal structure of providencia alcalifaciens 3-dehydroquinate synthase (dhqs) in complex with MG2+, NAD and chlorogenic acid
Analyse Crystal structure of providencia alcalifaciens 3-dehydroquinate synthase (dhqs)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LK2
- Type
- protein
- Length
- 1,397 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate synthase
- EC
- 4.2.3.4
- UniProt
- X6Q997
- Ligands
- NAD, 7LH, MG
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 357 | 50% helix, 20% strand | X6Q997 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 358 | 50% helix, 20% strand | X6Q997 |
| C | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 344 | 49% helix, 21% strand | X6Q997 |
| D | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 338 | 50% helix, 21% strand | X6Q997 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 7LH · (1R,3R,4S,5R)-3-[3-[3,4-bis(oxidanyl)phenyl]propanoyloxy]-1,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.76 | 0.80 | 68 | NAD, 7LH |
| 2 | 785 | 0.75 | 0.79 | 66 | NAD, 7LH |
| 3 | 832 | 0.74 | 0.78 | 67 | NAD, MG, 7LH |
| 4 | 971 | 0.73 | 0.77 | 77 | NAD, MG, 7LH |
| 5 | 62 | 0.70 | 0.96 | 21 | EDO |
Interfaces
4 interfaces between chains.
- A–C · 1197 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1190 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1051 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LK2 · Crystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in… · 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 X6Q997
- Elsewhere: RCSB PDB 6LK2 · PDBe 6LK2 · UniProt X6Q997
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