MolNFT v1 · #24947 · protein
Crystal structure of the heme pas sensor domain of ec dos (oxygen- bound form)
1VB6 · Heme pas sensor protein: “Crystal structure of the heme pas sensor domain of ec dos (oxygen- bound form)”. X-ray diffraction, 2 ligands (HEM, OXY), 3 pockets (best druggability 0.71). MolNFT v1 #24947 on GenesisL1: 3D structure…
- PDB
- 1VB6
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme pas sensor protein
- UniProt
- P76129
- Ligands
- HEM, OXY
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heme pas sensor protein | protein | 114 | 28% helix, 33% strand | P76129 |
| B | Heme pas sensor protein | protein | 110 | 30% helix, 39% strand | P76129 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · chains B
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 | 217 | 0.71 | 0.87 | 28 | HEM, OXY |
| 2 | 213 | 0.68 | 0.85 | 27 | HEM |
| 3 | 60 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1223 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1VB6 · Crystal Structure of the heme PAS sensor domain of Ec DOS (oxygen-bound form) · the same entry in another collection · chain A against A, TM-score 1.00
- P76129 · AlphaFold monomer V2.0 prediction for oxygen sensor protein dosp (P76129) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 1VB6 · PDBe 1VB6 · UniProt P76129
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