MolNFT v1 · #140417 · protein
Crystal structure of lsrk-hpr complex with ADP
5YA2 · Autoinducer-2 kinase: “Crystal structure of lsrk-hpr complex with ADP”. X-ray diffraction, 2 ligands (ADP, PO4), 13 pockets (best druggability 0.74). MolNFT v1 #140417 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YA2
- Type
- protein
- Length
- 1,126 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autoinducer-2 kinase; Phosphocarrier protein hpr
- EC
- 2.7.1.189, 2.7.11.-
- UniProt
- P77432, P0AA04
- Ligands
- ADP, PO4
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Autoinducer-2 kinase (EC 2.7.1.189) | protein | 478 | 45% helix, 21% strand | P77432 |
| C, D | Phosphocarrier protein hpr (EC 2.7.11.-) | protein | 85 | 34% helix, 27% strand | P0AA04 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
- HEZ · Hexane-1,6-diol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.74 | 0.79 | 84 | HEZ, PO4 |
| 2 | 549 | 0.70 | 0.79 | 59 | ADP |
| 3 | 386 | 0.64 | 0.78 | 47 | empty |
| 4 | 139 | 0.50 | 0.79 | 22 | ADP |
| 5 | 123 | 0.45 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 732 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 713 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 675 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YA2 · Crystal structure of LsrK-HPr complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P0AA04 · AlphaFold monomer V2.0 prediction for phosphocarrier protein hpr (P0AA04) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P77432 · AlphaFold monomer V2.0 prediction for autoinducer-2 kinase (P77432) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P77432
- Every structure of UniProt P0AA04
- Elsewhere: RCSB PDB 5YA2 · PDBe 5YA2 · UniProt P77432 · UniProt P0AA04
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