MolNFT v1 · #1539 · protein
Protocatechuate 4,5-dioxygenase (ligab) in complex with protocatechuate (pca)
1B4U: “Protocatechuate 4,5-dioxygenase (ligab) in complex with protocatechuate (pca)”. X-ray diffraction, 2 ligands (DHB, FE), 9 pockets (best druggability 0.72). MolNFT v1 #1539 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1B4U
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocatechuate 4,5-dioxygenase
- EC
- 1.13.11.8
- UniProt
- P22635, P22636
- Ligands
- DHB, FE
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protocatechuate 4,5-dioxygenase (EC 1.13.11.8) | protein | 132 | 61% helix, 1% strand | P22635 |
| B, D | Protocatechuate 4,5-dioxygenase (EC 1.13.11.8) | protein | 298 | 35% helix, 24% strand | P22636 |
Ligands and binding sites
- DHB · 3,4-dihydroxybenzoic acid · ligand · 2 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.72 | 0.99 | 20 | empty |
| 2 | 213 | 0.69 | 0.86 | 36 | DHB |
| 3 | 259 | 0.67 | 0.83 | 48 | FE, DHB |
| 4 | 244 | 0.46 | 0.72 | 31 | empty |
| 5 | 111 | 0.40 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2176 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2149 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1280 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1B4U · Protocatechuate 4,5-dioxygenase (ligab) in complex with protocatechuate (pca) · the same entry in another collection · chain A against A, TM-score 1.00
- P22636 · AlphaFold monomer V2.0 prediction for protocatechuate 4,5-dioxygenase beta chain (P22636) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P22635 · AlphaFold monomer V2.0 prediction for protocatechuate 4,5-dioxygenase alpha chain (P22635) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P22635
- Every structure of UniProt P22636
- Elsewhere: RCSB PDB 1B4U · PDBe 1B4U · UniProt P22635 · UniProt P22636
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