MolNFT v1 · #176314 · protein
Crystal structure of thermoglobin Y29F mutant in complex with imidazole
7DIH: “Crystal structure of thermoglobin Y29F mutant in complex with imidazole”. X-ray diffraction, 2 ligands (HEM, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #176314 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DIH
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermoglobin
- UniProt
- O66586
- Ligands
- HEM, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermoglobin | protein | 139 | 82% helix, 0% strand | O66586 |
| B | Thermoglobin | protein | 137 | 83% helix, 0% strand | O66586 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.75 | 0.84 | 37 | HEM, IMD |
| 2 | 451 | 0.75 | 0.84 | 39 | HEM, IMD |
| 3 | 64 | 0.28 | 0.73 | 18 | empty |
| 4 | 53 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 493 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7DIH · Crystal structure of Thermoglobin Y29F mutant in complex with imidazole · the same entry in another collection · chain A against A, TM-score 1.00
- O66586 · AlphaFold monomer V2.0 prediction for uncharacterized globin-like protein AQ_211 (O66586) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O66586
- Elsewhere: RCSB PDB 7DIH · PDBe 7DIH · UniProt O66586
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