Research workbench
Crystal structure of heme domain of direct oxygen sensor from E. COLI
Analyse Crystal structure of heme domain of direct oxygen sensor from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S67
- 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 · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Hypothetical protein yddu | protein | 119 | 28% 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 | 236 | 0.69 | 0.85 | 30 | HEM |
| 2 | 224 | 0.68 | 0.85 | 29 | HEM, OXY |
| 3 | 61 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- L–U · 1303 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1S67 · 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 1S67 · PDBe 1S67 · UniProt P76129
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