Research workbench
Structure of 3-dehydroquinate synthase from actinidia chinensis in complex with NAD
Analyse Structure of 3-dehydroquinate synthase from actinidia chinensis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZOK
- Type
- protein
- Length
- 1,460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate synthase
- EC
- 4.2.3.4
- Ligands
- GLY, NAD, PO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-dehydroquinate synthase (EC 4.2.3.4) | protein | 365 | 51% helix, 19% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 5 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, D, C
- 2PE · Nonaethylene glycol · additive · chains B, D
- PGE · Triethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.85 | 0.87 | 97 | PO4, NAD, 2PE, GLY |
| 2 | 604 | 0.83 | 0.88 | 73 | PO4, NAD |
| 3 | 1075 | 0.82 | 0.83 | 83 | PEG |
| 4 | 427 | 0.79 | 0.88 | 60 | PO4, NAD, GLY |
| 5 | 434 | 0.79 | 0.87 | 55 | PO4, NAD, GLY |
Interfaces
5 interfaces between chains.
- C–D · 1980 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1966 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 376 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZOK · Structure of 3-Dehydroquinate Synthase from Actinidia chinensis in complex with NAD · 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
- Elsewhere: RCSB PDB 3ZOK · PDBe 3ZOK
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