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Structure of chea domain P4 in complex with an ADP analog
Analyse Structure of chea domain P4 in complex with an ADP analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MI6
- Type
- protein
- Length
- 729 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemotaxis protein chea
- EC
- 2.7.13.3
- UniProt
- Q56310
- Ligands
- JSJ, ADP, SO4
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chemotaxis protein chea (EC 2.7.13.3) | protein | 183 | 43% helix, 25% strand | Q56310 |
| B | Chemotaxis protein chea (EC 2.7.13.3) | protein | 187 | 40% helix, 24% strand | Q56310 |
| C | Chemotaxis protein chea (EC 2.7.13.3) | protein | 184 | 41% helix, 22% strand | Q56310 |
| D | Chemotaxis protein chea (EC 2.7.13.3) | protein | 175 | 42% helix, 26% strand | Q56310 |
Ligands and binding sites
- JSJ · 5'-O-[(S)-hydroxy{[(s)-hydroxy{[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl) methyl]disulfanyl}phosphoryl]oxy}phosphoryl]adenosine · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.72 | 0.81 | 43 | JSJ |
| 2 | 415 | 0.65 | 0.79 | 49 | SO4 |
| 3 | 475 | 0.64 | 0.77 | 46 | SO4 |
| 4 | 471 | 0.63 | 0.77 | 47 | ADP |
| 5 | 298 | 0.59 | 0.78 | 35 | JSJ |
Interfaces
3 interfaces between chains.
- A–B · 1301 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1182 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1089 Ų buried · 11 hydrogen bonds · protein-protein
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 Q56310
- Elsewhere: RCSB PDB 6MI6 · PDBe 6MI6 · UniProt Q56310
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