MolNFT v1 · #121393 · protein
Non-covalent complex of and dahp synthase and chorismate mutase from corynebacterium glutamicum with bound transition state analog
5HUD · 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase: “Non-covalent complex of and dahp synthase and chorismate mutase from corynebacterium glutamicum with bound…”. X-ray diffraction, 4 ligands (TRP, TSA, MN), 20 pockets…
- PDB
- 5HUD
- Type
- protein
- Length
- 2,134 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase; Chorismate mutase
- EC
- 5.4.99.5
- UniProt
- Q8NNL5, Q8NS29
- Ligands
- TRP, TSA, MN, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase | protein | 444 | 45% helix, 14% strand | Q8NNL5 |
| C | 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase | protein | 456 | 45% helix, 13% strand | Q8NNL5 |
| D | 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase | protein | 457 | 46% helix, 14% strand | Q8NNL5 |
| E | Chorismate mutase (EC 5.4.99.5) | protein | 84 | 85% helix, 0% strand | Q8NS29 |
| F, G, H | Chorismate mutase (EC 5.4.99.5) | protein | 83 | 81% helix, 0% strand | Q8NS29 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains A, D, B, C
- TSA · 8-hydroxy-2-oxa-bicyclo[3.3.1]non-6-ene-3,5-dicarboxylic acid · ligand · 4 copies · chains E, F, G, H
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 66 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 16 copies · chains A, B, C, D, G, H
- PGE · Triethylene glycol · additive · 14 copies · chains C, D, E, F, G
- PG4 · Tetraethylene glycol · additive · 5 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.82 | 0.84 | 48 | empty |
| 2 | 986 | 0.81 | 0.82 | 85 | PEG, TRP, GOL |
| 3 | 939 | 0.80 | 0.82 | 81 | empty |
| 4 | 877 | 0.80 | 0.82 | 83 | GOL, PEG, TRP, PG4 |
| 5 | 97 | 0.69 | 0.93 | 21 | TSA |
Interfaces
12 interfaces between chains.
- G–H · 2249 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2242 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1062 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1038 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1020 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5HUD · Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium… · 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 Q8NNL5
- Every structure of UniProt Q8NS29
- Elsewhere: RCSB PDB 5HUD · PDBe 5HUD · UniProt Q8NNL5 · UniProt Q8NS29
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