MolNFT v1 · #21320 · protein
Crystal structure of heme domain of direct oxygen sensor from E. COLI
1S66 · Hypothetical protein yddu: “Crystal structure of heme domain of direct oxygen sensor from E. COLI”. X-ray diffraction, 2 ligands (HEM, OXY), 3 pockets (best druggability 0.69). MolNFT v1 #21320 on GenesisL1: 3D structure, binding…
- PDB
- 1S66
- Type
- protein
- Length
- 234 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yddu
- UniProt
- P76129
- Ligands
- HEM, OXY
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Hypothetical protein yddu | protein | 119 | 25% helix, 31% strand | P76129 |
| U | Hypothetical protein yddu | protein | 115 | 30% helix, 33% strand | P76129 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains L, U
- OXY · Oxygen molecule · ion · chains L
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 | 241 | 0.69 | 0.85 | 31 | HEM, OXY |
| 2 | 221 | 0.69 | 0.85 | 26 | HEM |
| 3 | 52 | 0.24 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- L–U · 1313 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1S66 · Crystal structure of heme domain of direct oxygen sensor from E. coli · the same entry in another collection · chain L against L, TM-score 1.00
- P76129 · AlphaFold monomer V2.0 prediction for oxygen sensor protein dosp (P76129) · a predicted model of the same protein · chain U against A, TM-score 0.93
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 P76129
- Elsewhere: RCSB PDB 1S66 · PDBe 1S66 · UniProt P76129
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