MolNFT v1 · #28648 · protein
Protocatechuate 3,4-dioxygenase Y408E mutant
1YKM · Protocatechuate 3,4-dioxygenase alpha chain: “Protocatechuate 3,4-dioxygenase Y408E mutant”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.82). MolNFT v1 #28648 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1YKM
- 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
- FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 31% 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 | 9% 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, 30% strand | P00437 |
Ligands and binding sites
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.82 | 0.84 | 86 | empty |
| 2 | 898 | 0.81 | 0.83 | 89 | empty |
| 3 | 129 | 0.80 | 0.98 | 40 | empty |
| 4 | 794 | 0.80 | 0.83 | 77 | empty |
| 5 | 538 | 0.80 | 0.86 | 55 | empty |
Interfaces
35 interfaces between chains.
- I–J · 3784 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 3774 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 3773 Ų buried · 65 hydrogen bonds · protein-protein
- K–L · 3764 Ų buried · 69 hydrogen bonds · protein-protein
- E–F · 3764 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 1YKM · Protocatechuate 3,4-Dioxygenase Y408E mutant · 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 1YKM · PDBe 1YKM · UniProt P00436 · UniProt P00437
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