Research workbench
Non-covalent complex between dahp synthase and chorismate mutase from mycobacterium tuberculosis with bound tsa
Analyse Non-covalent complex between dahp synthase and chorismate mutase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W1A
- Type
- protein
- Length
- 1,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog; Chorismate mutase
- EC
- 2.5.1.54, 5.4.99.5
- UniProt
- O53512, P64767
- Ligands
- TSA, CE1, MN, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 451 | 44% helix, 15% strand | O53512 |
| B | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 449 | 43% helix, 16% strand | O53512 |
| C | Chorismate mutase (EC 5.4.99.5) | protein | 78 | 77% helix, 0% strand | P64767 |
| D | Chorismate mutase (EC 5.4.99.5) | protein | 79 | 77% helix, 0% strand | P64767 |
Ligands and binding sites
- TSA · 8-hydroxy-2-oxa-bicyclo[3.3.1]non-6-ene-3,5-dicarboxylic acid · ligand · 2 copies · chains C, D
- CE1 · O-dodecanyl octaethylene glycol · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.78 | 0.85 | 63 | CE1, PG4 |
| 2 | 326 | 0.62 | 0.79 | 37 | SO4 |
| 3 | 267 | 0.62 | 0.81 | 32 | empty |
| 4 | 315 | 0.62 | 0.79 | 41 | SO4, GOL |
| 5 | 269 | 0.57 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1639 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 885 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2W1A · Non-covalent complex between dahp synthase and chorismate mutase from Mycobacterium… · the same entry in another collection · chain A against A, 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
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 P64767
- Elsewhere: RCSB PDB 2W1A · PDBe 2W1A · UniProt O53512 · UniProt P64767
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