MolNFT v2 · #227505 · protein
DosP R97A with c-di-GMP
9CLO · Oxygen sensor protein DosP: “DosP R97A with c-di-GMP”. Electron microscopy at 3.1, 3 ligands (HEM, C2E, MG), 15 pockets (best druggability 0.79). MolNFT v2 #227505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 9CLO
- Type
- protein
- Length
- 1,574 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Escherichia coli
- Molecule
- Oxygen sensor protein DosP
- EC
- 3.1.4.52
- UniProt
- P76129
- Ligands
- HEM, C2E, MG
- Pockets
- 15 · best druggability 0.79
Structure
electron microscopy · resolution 3.1 · 1 distinct chain · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxygen sensor protein DosP (EC 3.1.4.52) | protein | 787 | 42% helix, 25% strand | P76129 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.79 | 0.80 | 98 | empty |
| 2 | 743 | 0.75 | 0.80 | 85 | empty |
| 3 | 282 | 0.70 | 0.84 | 35 | HEM |
| 4 | 357 | 0.69 | 0.82 | 34 | HEM |
| 5 | 421 | 0.63 | 0.77 | 38 | C2E, MG |
Interfaces
1 interface between chains.
- A–B · 5086 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- P76129 · AlphaFold monomer V2.0 prediction for oxygen sensor protein dosp (P76129) · a predicted model of the same protein · chain A against A, TM-score 0.46
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 9CLO · PDBe 9CLO · UniProt P76129
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