MolNFT v1 · #115467 · protein
Dahp (3-deoxy-D-arabinoheptulosonate-7-phosphate) synthase in complex with dahp oxime.
5CKS · Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive: “Dahp (3-deoxy-D-arabinoheptulosonate-7-phosphate) synthase in complex with dahp oxime.”. X-ray diffraction, 2 ligands (52L, GAL), 8 pockets (best druggability 0.87).…
- PDB
- 5CKS
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive
- EC
- 2.5.1.54
- UniProt
- P0AB91
- Ligands
- 52L, GAL
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 339 | 41% helix, 20% strand | P0AB91 |
| B, D | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 345 | 41% helix, 19% strand | P0AB91 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (EC 2.5.1.54) | protein | 343 | 41% helix, 19% strand | P0AB91 |
Ligands and binding sites
- 52L · DAHP Oxime · ligand · 2 copies · chains B, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.87 | 0.88 | 152 | GAL |
| 2 | 551 | 0.83 | 0.89 | 87 | GAL |
| 3 | 572 | 0.74 | 0.81 | 74 | 52L |
| 4 | 591 | 0.73 | 0.80 | 78 | 52L |
| 5 | 53 | 0.71 | 0.99 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2879 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2847 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 587 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 569 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 56 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5CKS · DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase in complex with DAHP Oxime. · the same entry in another collection · chain D against D, TM-score 1.00
- P0AB91 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase… · a predicted model of the same protein · chain B 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 P0AB91
- Elsewhere: RCSB PDB 5CKS · PDBe 5CKS · UniProt P0AB91
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