MolNFT v1 · #155879 · protein
Crystal structure of providencia alcalifaciens 3-dehydroquinate synthase (dhqs) in complex with MG2+ and NAD
6LLA: “Crystal structure of providencia alcalifaciens 3-dehydroquinate synthase (dhqs) in complex with MG2+ and NAD”. X-ray diffraction, 2 ligands (NAD, MG), 12 pockets (best druggability 0.75). MolNFT v1 #155879 on GenesisL1: 3D…
- PDB
- 6LLA
- Type
- protein
- Length
- 1,432 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, MG
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 362 | 49% helix, 20% strand | X6Q997 |
| B | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 363 | 48% helix, 20% strand | X6Q997 |
| C | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 354 | 49% helix, 22% strand | X6Q997 |
| D | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 353 | 50% helix, 22% strand | X6Q997 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 31 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.75 | 0.80 | 60 | NAD, EDO |
| 2 | 813 | 0.75 | 0.79 | 77 | NAD, EDO |
| 3 | 918 | 0.74 | 0.78 | 67 | PEG, NAD, EDO |
| 4 | 988 | 0.74 | 0.77 | 73 | NAD, MG, PEG |
| 5 | 65 | 0.71 | 0.97 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1223 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1211 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 947 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LLA · 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 6LLA · PDBe 6LLA · UniProt X6Q997
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