Research workbench
Structure of protoporphyrinogen oxidase from myxococcus xanthus
Analyse Structure of protoporphyrinogen oxidase from myxococcus xanthus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IVE
- Type
- protein
- Length
- 901 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoporphyrinogen oxidase
- UniProt
- P56601
- Ligands
- TWN, FAD
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protoporphyrinogen oxidase | protein | 451 | 39% helix, 24% strand | P56601 |
| B | Protoporphyrinogen oxidase | protein | 450 | 40% helix, 25% strand | P56601 |
Ligands and binding sites
- TWN · (3S)-3-[(2S,3S,4R)-3,4-dimethyltetrahydrofuran-2-yl]butyl laurate · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.83 | 0.84 | 95 | FAD, TWN |
| 2 | 1027 | 0.81 | 0.82 | 96 | FAD, TWN |
| 3 | 281 | 0.58 | 0.77 | 23 | empty |
| 4 | 61 | 0.54 | 0.88 | 17 | empty |
| 5 | 116 | 0.47 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2IVE · Structure of protoporphyrinogen oxidase from Myxococcus xanthus · the same entry in another collection · chain A against A, TM-score 1.00
- P56601 · AlphaFold monomer V2.0 prediction for coproporphyrinogen III oxidase (P56601) · a predicted model of the same protein · chain A against A, 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 P56601
- Elsewhere: RCSB PDB 2IVE · PDBe 2IVE · UniProt P56601
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