Research workbench
The structure of the C-terminal heme nitrobindin domain of thap domain-containing protein 4 from homo sapiens
Analyse The structure of the C-terminal heme nitrobindin domain of thap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IA8
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thap domain-containing protein 4
- UniProt
- Q8WY91
- Ligands
- HEM
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thap domain-containing protein 4 | protein | 162 | 6% helix, 64% strand | Q8WY91 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.68 | 0.80 | 46 | HEM |
| 2 | 442 | 0.68 | 0.79 | 42 | HEM |
| 3 | 141 | 0.48 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1331 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3IA8 · The structure of the C-terminal heme nitrobindin domain of THAP domain-containing protein… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WY91 · AlphaFold monomer V2.0 prediction for peroxynitrite isomerase THAP4 (Q8WY91) · 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 Q8WY91
- Elsewhere: RCSB PDB 3IA8 · PDBe 3IA8 · UniProt Q8WY91
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