Research workbench
Protocatechuate 3,4-dioxygenase Y408H mutant bound to dhb
Analyse Protocatechuate 3,4-dioxygenase Y408H mutant bound to dhb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YKP
- Type
- protein
- Length
- 2,628 residues
- Chains
- 12
- 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
- DHB, FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3) | protein | 200 | 10% helix, 32% strand | P00436 |
| B, D, F, H, J, L | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 8% helix, 29% strand | P00437 |
Ligands and binding sites
- DHB · 3,4-dihydroxybenzoic acid · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- FE · Fe (III) ion · metal · 6 copies · chains B, D, F, H, J, L
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 | 983 | 0.84 | 0.85 | 92 | DHB |
| 2 | 800 | 0.82 | 0.85 | 80 | empty |
| 3 | 940 | 0.82 | 0.84 | 87 | empty |
| 4 | 831 | 0.81 | 0.83 | 77 | DHB |
| 5 | 615 | 0.80 | 0.85 | 60 | DHB |
Interfaces
35 interfaces between chains.
- K–L · 3777 Ų buried · 65 hydrogen bonds · protein-protein
- I–J · 3751 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 3748 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 3730 Ų buried · 62 hydrogen bonds · protein-protein
- G–H · 3727 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 1YKP · Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB · the same entry in another collection · chain L against L, 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 1YKP · PDBe 1YKP · UniProt P00436 · UniProt P00437
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