Research workbench
Hthp: a hexameric tyrosine-coordinated heme protein
Analyse Hthp: a hexameric tyrosine-coordinated heme protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OYY
- Type
- protein
- Length
- 568 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexameric cytochrome
- UniProt
- Q5LL55
- Ligands
- HEM, IOD
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Hexameric cytochrome | protein | 71 | 72% helix, 0% strand | Q5LL55 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, F, G, E, H
- IOD · Iodide ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.80 | 0.81 | 69 | empty |
| 2 | 1028 | 0.80 | 0.81 | 78 | IOD, HEM |
| 3 | 177 | 0.66 | 0.85 | 24 | IOD, HEM |
| 4 | 191 | 0.65 | 0.85 | 25 | IOD, HEM |
| 5 | 173 | 0.65 | 0.85 | 22 | IOD, HEM |
Interfaces
9 interfaces between chains.
- G–H · 1147 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1132 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1131 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 1129 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2OYY · HTHP: a hexameric tyrosine-coordinated heme protein · 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 Q5LL55
- Elsewhere: RCSB PDB 2OYY · PDBe 2OYY · UniProt Q5LL55
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