MolNFT v1 · #113459 · protein
Chorismatase mechanisms reveal fundamentally different types of reaction in a single conserved protein fold
5AG3 · Putative pteridine-dependent dioxygenase: “Chorismatase mechanisms reveal fundamentally different types of reaction in a single conserved protein fold”. X-ray diffraction, 2 ligands (3EB, SO4), 12 pockets (best druggability 0.78).…
- PDB
- 5AG3
- Type
- protein
- Length
- 1,000 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pteridine-dependent dioxygenase
- UniProt
- O30478
- Ligands
- 3EB, SO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative pteridine-dependent dioxygenase | protein | 333 | 23% helix, 35% strand | O30478 |
| B | Putative pteridine-dependent dioxygenase | protein | 332 | 24% helix, 35% strand | O30478 |
| C | Putative pteridine-dependent dioxygenase | protein | 335 | 23% helix, 35% strand | O30478 |
Ligands and binding sites
- 3EB · 3-(2-carboxyethyl)benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 13 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.78 | 0.97 | 30 | empty |
| 2 | 124 | 0.75 | 0.94 | 33 | 3EB |
| 3 | 150 | 0.72 | 0.91 | 38 | 3EB |
| 4 | 600 | 0.63 | 0.75 | 60 | SO4, PEG |
| 5 | 122 | 0.56 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 174 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 76 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5AG3 · Chorismatase mechanisms reveal fundamentally different types of reaction in a single… · the same entry in another collection · chain A against A, TM-score 1.00
- O30478 · AlphaFold monomer V2.0 prediction for 3-hydroxybenzoate synthase (O30478) · 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 O30478
- Elsewhere: RCSB PDB 5AG3 · PDBe 5AG3 · UniProt O30478
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