Research workbench
Crystal structure of coproporphyrinogen III oxidase
Analyse Crystal structure of coproporphyrinogen III oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TXN
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coproporphyrinogen III oxidase
- EC
- 1.3.3.3
- UniProt
- P11353
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coproporphyrinogen III oxidase (EC 1.3.3.3) | protein | 259 | 38% helix, 27% strand | P11353 |
| B | Coproporphyrinogen III oxidase (EC 1.3.3.3) | protein | 256 | 39% helix, 27% strand | P11353 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.83 | 0.85 | 87 | GOL |
| 2 | 97 | 0.49 | 0.82 | 18 | empty |
| 3 | 86 | 0.45 | 0.81 | 16 | empty |
| 4 | 60 | 0.43 | 0.82 | 21 | empty |
| 5 | 52 | 0.34 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2943 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 1TXN · Crystal structure of coproporphyrinogen III oxidase · the same entry in another collection · chain A against A, TM-score 1.00
- P11353 · AlphaFold monomer V2.0 prediction for oxygen-dependent coproporphyrinogen-III oxidase… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P11353
- Elsewhere: RCSB PDB 1TXN · PDBe 1TXN · UniProt P11353
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