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Structure of protocatechuate 3,4-dioxygenase complexed with 3-fluro-4- hydroxybenzoate
Analyse Structure of protocatechuate 3,4-dioxygenase complexed with 3-fluro-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PCF
- Type
- protein
- Length
- 2,598 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocatechuate 3,4-dioxygenase
- EC
- 1.13.11.3
- UniProt
- P00436, P00437
- Ligands
- FHB, FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) | protein | 200 | 14% helix, 32% strand | P00436 |
| M, N, O, P, Q, R | Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) | protein | 233 | 9% helix, 30% strand | P00437 |
Ligands and binding sites
- FHB · 3-fluoro-4-hydroxybenzoic acid · ligand · 12 copies · chains A, M, O, B, N, C, D, P, R, E, Q, F
- FE · Fe (III) ion · metal · 6 copies · chains M, N, O, P, Q, R
- BME · Beta-mercaptoethanol · additive · 6 copies · chains M, N, O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.82 | 0.86 | 82 | FHB |
| 2 | 745 | 0.81 | 0.85 | 83 | FHB |
| 3 | 112 | 0.79 | 0.98 | 34 | empty |
| 4 | 458 | 0.79 | 0.87 | 49 | FHB |
| 5 | 603 | 0.78 | 0.84 | 51 | FHB |
Interfaces
35 interfaces between chains.
- C–O · 3673 Ų buried · 69 hydrogen bonds · protein-protein
- D–P · 3667 Ų buried · 73 hydrogen bonds · protein-protein
- B–N · 3662 Ų buried · 63 hydrogen bonds · protein-protein
- F–R · 3660 Ų buried · 64 hydrogen bonds · protein-protein
- A–M · 3652 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 3PCF · Structure of protocatechuate 3,4-dioxygenase complexed with 3-fluro-4-hydroxybenzoate · the same entry in another collection · chain P against P, TM-score 1.00
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 3PCF · PDBe 3PCF · UniProt P00436 · UniProt P00437
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