MolNFT v1 · #123683 · protein
Crystal structure of FE(II) unliganded H-nox protein from C. subterraneus
5JRU · Methyl-accepting chemotaxis protein: “Crystal structure of FE(II) unliganded H-nox protein from C. subterraneus”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.85). MolNFT v1 #123683 on GenesisL1: 3D structure…
- PDB
- 5JRU
- Type
- protein
- Length
- 1,115 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis protein
- UniProt
- Q8RBX6
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Methyl-accepting chemotaxis protein | protein | 186 | 51% helix, 21% strand | Q8RBX6 |
| B | Methyl-accepting chemotaxis protein | protein | 185 | 51% helix, 19% strand | Q8RBX6 |
| C | Methyl-accepting chemotaxis protein | protein | 184 | 52% helix, 20% strand | Q8RBX6 |
| D, F | Methyl-accepting chemotaxis protein | protein | 187 | 51% helix, 21% strand | Q8RBX6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.85 | 0.95 | 35 | HEM |
| 2 | 343 | 0.85 | 0.94 | 37 | HEM |
| 3 | 332 | 0.85 | 0.94 | 37 | HEM |
| 4 | 324 | 0.85 | 0.94 | 35 | HEM |
| 5 | 352 | 0.85 | 0.93 | 36 | HEM |
Interfaces
9 interfaces between chains.
- B–F · 1008 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 972 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 934 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 929 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 864 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5JRU · Crystal structure of Fe(II) unliganded H-NOX protein from C. subterraneus · 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 Q8RBX6
- Elsewhere: RCSB PDB 5JRU · PDBe 5JRU · UniProt Q8RBX6
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