Research workbench
Crystal structure of anabaena sp. dyp-type peroxidese (anapx)
Analyse Crystal structure of anabaena sp. dyp-type peroxidese (anapx) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C2I
- Type
- protein
- Length
- 1,850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALR1585 protein
- UniProt
- Q8YWM0
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALR1585 protein | protein | 468 | 34% helix, 19% strand | Q8YWM0 |
| B | ALR1585 protein | protein | 460 | 33% helix, 20% strand | Q8YWM0 |
| C, D | ALR1585 protein | protein | 461 | 33% helix, 20% strand | Q8YWM0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
- ACY · Acetic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.84 | 0.94 | 43 | HEM |
| 2 | 309 | 0.84 | 0.94 | 44 | HEM |
| 3 | 293 | 0.84 | 0.94 | 37 | HEM |
| 4 | 298 | 0.83 | 0.94 | 44 | HEM |
| 5 | 1065 | 0.82 | 0.83 | 97 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1230 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1222 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 780 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5C2I · Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX) · 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 Q8YWM0
- Elsewhere: RCSB PDB 5C2I · PDBe 5C2I · UniProt Q8YWM0
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