Research workbench
Non-covalent complex of dahp synthase and chorismate mutase from mycobacterium tuberculosis with bound transition state analog and feedback effectors tyrosine and phenylalanine
Analyse Non-covalent complex of dahp synthase and chorismate mutase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CKX
- Type
- protein
- Length
- 1,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase arog; Intracellular chorismate mutase
- EC
- 2.5.1.54, 5.4.99.5
- UniProt
- O53512, P9WIC1
- Ligands
- PHE, TSA, TYR, MN, SO4, CL
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase arog (EC 2.5.1.54) | protein | 448 | 44% helix, 15% strand | O53512 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase arog (EC 2.5.1.54) | protein | 452 | 43% helix, 15% strand | O53512 |
| C | Intracellular chorismate mutase (EC 5.4.99.5) | protein | 78 | 83% helix, 0% strand | P9WIC1 |
| D | Intracellular chorismate mutase (EC 5.4.99.5) | protein | 79 | 78% helix, 0% strand | P9WIC1 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains A, B
- TSA · 8-hydroxy-2-oxa-bicyclo[3.3.1]non-6-ene-3,5-dicarboxylic acid · ligand · 2 copies · chains C, D
- TYR · Tyrosine · ligand · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.70 | 0.91 | 21 | PHE |
| 2 | 194 | 0.69 | 0.86 | 21 | PHE |
| 3 | 251 | 0.61 | 0.81 | 29 | GOL |
| 4 | 279 | 0.60 | 0.79 | 40 | SO4 |
| 5 | 141 | 0.59 | 0.84 | 24 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1747 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 909 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 908 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5CKX · Non-covalent complex of DAHP synthase and chorismate mutase from Mycobacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- O53512 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase arog… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P9WIC1 · AlphaFold monomer V2.0 prediction for intracellular chorismate mutase (P9WIC1) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O53512
- Every structure of UniProt P9WIC1
- Elsewhere: RCSB PDB 5CKX · PDBe 5CKX · UniProt O53512 · UniProt P9WIC1
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