MolNFT v1 · #94114 · protein
Crystal structure of phzg from burkholderia lata 383 in complex with tetrahydrophenazine-1-carboxylic acid
4HMX · Pyridoxamine 5'-phosphate oxidase: “Crystal structure of phzg from burkholderia lata 383 in complex with tetrahydrophenazine-1-carboxylic acid”. X-ray diffraction, 2 ligands (FMN, WUB), 3 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 4HMX
- Type
- protein
- Length
- 405 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine 5'-phosphate oxidase
- EC
- 1.4.3.5
- UniProt
- Q396C5
- Ligands
- FMN, WUB
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) | protein | 202 | 28% helix, 37% strand | Q396C5 |
| B | Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) | protein | 203 | 29% helix, 35% strand | Q396C5 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- WUB · (1R,10aS)-1,2,10,10a-tetrahydrophenazine-1-carboxylic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.74 | 0.83 | 44 | FMN |
| 2 | 474 | 0.73 | 0.82 | 44 | WUB, FMN |
| 3 | 56 | 0.73 | 0.99 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2762 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 4HMX · Crystal structure of PhzG from Burkholderia lata 383 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q396C5 · AlphaFold monomer V2.0 prediction for dihydrophenazinedicarboxylate synthase (Q396C5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q396C5
- Elsewhere: RCSB PDB 4HMX · PDBe 4HMX · UniProt Q396C5
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