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Structure of protocatechuate 3,4-dioxygenase complexed with 3-iodo-4- hydroxybenzoate
Analyse Structure of protocatechuate 3,4-dioxygenase complexed with 3-iodo-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PCI
- 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
- IHB, FE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 30% 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 | 12% helix, 31% 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
- IHB · 3-iodo-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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.87 | 0.88 | 112 | IHB |
| 2 | 867 | 0.81 | 0.83 | 87 | IHB |
| 3 | 484 | 0.79 | 0.86 | 48 | IHB |
| 4 | 116 | 0.79 | 0.97 | 30 | empty |
| 5 | 719 | 0.78 | 0.83 | 65 | IHB |
Interfaces
35 interfaces between chains.
- B–N · 3666 Ų buried · 67 hydrogen bonds · protein-protein
- E–Q · 3666 Ų buried · 62 hydrogen bonds · protein-protein
- C–O · 3665 Ų buried · 66 hydrogen bonds · protein-protein
- D–P · 3648 Ų buried · 64 hydrogen bonds · protein-protein
- A–M · 3644 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 3PCI · Structure of protocatechuate 3,4-dioxygenase complexed with 3-iodo-4-hydroxybenzoate · the same entry in another collection · chain O against O, 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 3PCI · PDBe 3PCI · UniProt P00436 · UniProt P00437
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