MolNFT v1 · #62401 · protein
Probing the function of heme distortion in the H-nox family
3EEE · Methyl-accepting chemotaxis protein: “Probing the function of heme distortion in the H-nox family”. X-ray diffraction, 4 ligands (HEM, OXY, SO4), 13 pockets (best druggability 0.85). MolNFT v1 #62401 on GenesisL1: 3D structure…
- PDB
- 3EEE
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis protein
- UniProt
- Q8RBX6
- Ligands
- HEM, OXY, SO4, CL
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methyl-accepting chemotaxis protein | protein | 188 | 48% helix, 21% strand | Q8RBX6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
- CL · Chloride ion · ion · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.85 | 0.90 | 63 | HEM, OXY |
| 2 | 506 | 0.85 | 0.90 | 51 | HEM, OXY |
| 3 | 429 | 0.83 | 0.90 | 41 | HEM, OXY |
| 4 | 445 | 0.81 | 0.88 | 41 | HEM, OXY |
| 5 | 176 | 0.46 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 721 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 253 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 134 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EEE · Probing the function of heme distortion in the H-NOX family · 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 3EEE · PDBe 3EEE · UniProt Q8RBX6
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