MolNFT v1 · #70886 · protein
Tyrosine 447 of protocatechuate 3,4-dioxygenase controls efficient progress through catalysis
3LXV · Protocatechuate 3,4-dioxygenase alpha chain: “Tyrosine 447 of protocatechuate 3,4-dioxygenase controls efficient progress through catalysis”. X-ray diffraction, 5 ligands (4NC, FE, CO3), 19 pockets (best druggability 0.80). MolNFT…
- PDB
- 3LXV
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocatechuate 3,4-dioxygenase alpha chain; Protocatechuate 3,4-dioxygenase beta chain
- EC
- 1.13.11.3
- UniProt
- P00436, P00437
- Ligands
- 4NC, FE, CO3, SO4, CL
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3) | protein | 200 | 11% helix, 33% strand | P00436 |
| M, N, O | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 9% helix, 29% strand | P00437 |
Ligands and binding sites
- 4NC · 4-nitrocatechol · ligand · 4 copies · chains A, M, B, N, O, C
- FE · Fe (III) ion · metal · 3 copies · chains M, N, O
- CO3 · Carbonate ion · ion · 5 copies · chains A, M, N, O, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains B, C, N, O
- BME · Beta-mercaptoethanol · additive · 15 copies · chains A, M, N, B, C, O
- GOL · Glycerol · additive · 7 copies · chains A, M, O, N, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.80 | 0.83 | 76 | 4NC, CO3 |
| 2 | 996 | 0.79 | 0.81 | 79 | FE, BME, 4NC |
| 3 | 1005 | 0.79 | 0.81 | 77 | GOL, BME, 4NC |
| 4 | 490 | 0.75 | 0.83 | 49 | BME |
| 5 | 519 | 0.75 | 0.83 | 67 | empty |
Interfaces
15 interfaces between chains.
- B–N · 3717 Ų buried · 65 hydrogen bonds · protein-protein
- C–O · 3704 Ų buried · 65 hydrogen bonds · protein-protein
- A–M · 3693 Ų buried · 67 hydrogen bonds · protein-protein
- M–O · 340 Ų buried · 6 hydrogen bonds · protein-protein
- M–N · 326 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3LXV · Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through… · the same entry in another collection · chain O against O, TM-score 1.00
- P00437 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase beta chain (P00437) · a predicted model of the same protein · chain M against A, TM-score 1.00
- P00436 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase alpha chain (P00436) · 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 P00436
- Every structure of UniProt P00437
- Elsewhere: RCSB PDB 3LXV · PDBe 3LXV · UniProt P00436 · UniProt P00437
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