Research workbench
Structure of protocatechuate 3,4-dioxygenase complexed with 2- hydroxyisonicotinic acid N-oxide and cyanide
Analyse Structure of protocatechuate 3,4-dioxygenase complexed with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PCL
- 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
- INO, FE, CYN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 12% 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, 33% 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
- INO · 2-hydroxyisonicotinic acid N-oxide · ligand · 6 copies · chains A, M, B, N, C, O, D, P, E, Q, F, R
- FE · Fe (III) ion · metal · 6 copies · chains M, N, O, P, Q, R
- CYN · Cyanide ion · ion · 6 copies · chains A, M, B, N, C, O, D, P, E, Q, F, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.82 | 0.85 | 90 | empty |
| 2 | 779 | 0.81 | 0.84 | 85 | empty |
| 3 | 753 | 0.80 | 0.83 | 76 | CYN, FE, INO |
| 4 | 631 | 0.79 | 0.84 | 50 | CYN, FE, INO |
| 5 | 558 | 0.78 | 0.85 | 58 | CYN, FE, INO |
Interfaces
35 interfaces between chains.
- A–M · 3677 Ų buried · 70 hydrogen bonds · protein-protein
- B–N · 3673 Ų buried · 68 hydrogen bonds · protein-protein
- D–P · 3671 Ų buried · 67 hydrogen bonds · protein-protein
- F–R · 3663 Ų buried · 68 hydrogen bonds · protein-protein
- E–Q · 3659 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 3PCL · Structure of protocatechuate 3,4-dioxygenase complexed with 2-hydroxyisonicotinic acid… · 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 3PCL · PDBe 3PCL · UniProt P00436 · UniProt P00437
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