MolNFT v1 · #62505 · protein
Crystal structure of deskc-H188V in complex with AMP-pcp
3EHJ · Sensor kinase (yocf protein): “Crystal structure of deskc-H188V in complex with AMP-pcp”. X-ray diffraction, 2 ligands (ACP, CA), 3 pockets (best druggability 0.53). MolNFT v1 #62505 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EHJ
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor kinase (yocf protein)
- EC
- 2.7.13.3
- UniProt
- O34757
- Ligands
- ACP, CA
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 203 | 57% helix, 16% strand | O34757 |
| B | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 211 | 58% helix, 15% strand | O34757 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, 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 | 90 | 0.53 | 0.84 | 20 | ACP |
| 2 | 87 | 0.50 | 0.83 | 19 | ACP |
| 3 | 58 | 0.35 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1885 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
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 O34757
- Elsewhere: RCSB PDB 3EHJ · PDBe 3EHJ · UniProt O34757
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