Research workbench
Crystal structure of an H-nox protein from nostoc sp. pcc 7120, L66W mutant
Analyse Crystal structure of an H-nox protein from nostoc sp. pcc 7120, L66W mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TFD
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALR2278 protein
- UniProt
- Q8YUQ7
- Ligands
- HEM
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALR2278 protein | protein | 183 | 52% helix, 18% strand | Q8YUQ7 |
| B | ALR2278 protein | protein | 182 | 54% helix, 17% strand | Q8YUQ7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MLA · Malonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.84 | 0.91 | 58 | HEM |
| 2 | 459 | 0.83 | 0.90 | 64 | HEM |
| 3 | 161 | 0.55 | 0.81 | 26 | empty |
| 4 | 179 | 0.48 | 0.76 | 25 | MLA |
| 5 | 110 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3TFD · Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120, L66W 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 Q8YUQ7
- Elsewhere: RCSB PDB 3TFD · PDBe 3TFD · UniProt Q8YUQ7
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