MolNFT v1 · #60471 · protein
Structure of yeast chorismate mutase with bound TRP and an endooxabicyclic inhibitor
3CSM: “Structure of yeast chorismate mutase with bound TRP and an endooxabicyclic inhibitor”. X-ray diffraction, 2 ligands (TRP, TSA), 6 pockets (best druggability 0.76). MolNFT v1 #60471 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3CSM
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chorismate mutase
- EC
- 5.4.99.5
- UniProt
- P32178
- Ligands
- TRP, TSA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chorismate mutase (EC 5.4.99.5) | protein | 252 | 65% helix, 0% strand | P32178 |
Ligands and binding sites
- TRP · Tryptophan · 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 A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.76 | 0.94 | 23 | TSA |
| 2 | 127 | 0.74 | 0.94 | 23 | TSA |
| 3 | 500 | 0.65 | 0.77 | 49 | empty |
| 4 | 249 | 0.54 | 0.77 | 35 | empty |
| 5 | 144 | 0.47 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 518 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3CSM · Structure of yeast chorismate mutase with bound TRP and an endooxabicyclic inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- P32178 · AlphaFold monomer V2.0 prediction for chorismate mutase (P32178) · a predicted model of the same protein · chain A 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 P32178
- Elsewhere: RCSB PDB 3CSM · PDBe 3CSM · UniProt P32178
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