Research workbench
Crystal structure of chey-MG(2+)-BEF(3)(-) in complex with CHEZ(C19) peptide solved from a P2(1)2(1)2 crystal
Analyse Crystal structure of chey-MG(2+)-BEF(3)(-) in complex with CHEZ(C19) peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PL9
- Type
- protein
- Length
- 433 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemotaxis protein chey; Chemotaxis protein chez
- UniProt
- P0A2D5, P07800
- Ligands
- BEF, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chemotaxis protein chey | protein | 128 | 44% helix, 17% strand | P0A2D5 |
| D | Chemotaxis protein chez | protein | 19 | 53% helix, 5% strand | P07800 |
| E, F | Chemotaxis protein chez | protein | 15 | 67% helix, 0% strand | P07800 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.76 | 0.82 | 72 | MG, BEF |
| 2 | 139 | 0.46 | 0.77 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 545 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 540 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 499 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 389 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2PL9 · Crystal Structure of CheY-Mg(2+)-BeF(3)(-) in Complex with CheZ(C19) Peptide solved from… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A2D5 · AlphaFold monomer V2.0 prediction for chemotaxis protein chey (P0A2D5) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P07800 · AlphaFold monomer V2.0 prediction for protein phosphatase chez (P07800) · a predicted model of the same protein · chain F against A, TM-score 0.74
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 P0A2D5
- Every structure of UniProt P07800
- Elsewhere: RCSB PDB 2PL9 · PDBe 2PL9 · UniProt P0A2D5 · UniProt P07800
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