Research workbench
Coproporphyrinogen III oxidase (hemf) from acinetobacter baumannii
Analyse Coproporphyrinogen III oxidase (hemf) from acinetobacter baumannii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EO6
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coproporphyrinogen oxidase
- EC
- 1.3.3.3
- UniProt
- A0A0D5YE19
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coproporphyrinogen oxidase (EC 1.3.3.3) | protein | 312 | 45% helix, 25% strand | A0A0D5YE19 |
| B | Coproporphyrinogen oxidase (EC 1.3.3.3) | protein | 307 | 46% helix, 25% strand | A0A0D5YE19 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.83 | 0.86 | 65 | ACT |
| 2 | 784 | 0.82 | 0.85 | 63 | ACT |
| 3 | 128 | 0.40 | 0.74 | 19 | empty |
| 4 | 118 | 0.40 | 0.75 | 15 | empty |
| 5 | 102 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1435 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5EO6 · Coproporphyrinogen III oxidase (HemF) from Acinetobacter baumannii · the same entry in another collection · 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 A0A0D5YE19
- Elsewhere: RCSB PDB 5EO6 · PDBe 5EO6 · UniProt A0A0D5YE19
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