Research workbench
Microed structure of aeropyrum pernix protoglobin mutant
Analyse Microed structure of aeropyrum pernix protoglobin mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UTE
- Type
- protein
- Length
- 742 residues
- Chains
- 4
- Method
- electron crystallography
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protogloblin appgb
- UniProt
- Q9YFF4
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.85
Structure
electron crystallography · 2 distinct chains · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protogloblin appgb | protein | 190 | 61% helix, 2% strand | Q9YFF4 |
| B, C, D | Protogloblin appgb | protein | 184 | 64% helix, 2% strand | Q9YFF4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.85 | 0.93 | 41 | HEM, IMD |
| 2 | 357 | 0.82 | 0.91 | 39 | HEM, IMD |
| 3 | 357 | 0.81 | 0.90 | 41 | HEM, IMD |
| 4 | 408 | 0.79 | 0.87 | 45 | HEM, IMD |
| 5 | 708 | 0.66 | 0.75 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1782 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 569 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7UTE · MicroED structure of Aeropyrum pernix protoglobin mutant · 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 Q9YFF4
- Elsewhere: RCSB PDB 7UTE · PDBe 7UTE · UniProt Q9YFF4
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