Research workbench
Crystal structure of deskc in complex with AMP-pcp
Analyse Crystal structure of deskc in complex with AMP-pcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EHF
- Type
- protein
- Length
- 521 residues
- Chains
- 4
- 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, MG
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 179 | 58% helix, 18% strand | O34757 |
| B | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 104 | 79% helix, 2% strand | O34757 |
| C | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 57 | 89% helix, 0% strand | O34757 |
| D | Sensor kinase (yocf protein) (EC 2.7.13.3) | protein | 181 | 59% helix, 18% strand | O34757 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 3 copies · chains A, B, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.55 | 0.86 | 20 | ACP |
| 2 | 63 | 0.51 | 0.86 | 17 | ACP |
| 3 | 100 | 0.33 | 0.73 | 21 | empty |
| 4 | 51 | 0.27 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1520 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1328 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 125 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 1 hydrogen bond · 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 3EHF · PDBe 3EHF · UniProt O34757
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