MolNFT v1 · #140416 · protein
Crystal structure of lsrk-hpr complex with ATP
5YA1 · Autoinducer-2 kinase: “Crystal structure of lsrk-hpr complex with ATP”. X-ray diffraction, 2 ligands (ATP, PO4), 12 pockets (best druggability 0.75). MolNFT v1 #140416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YA1
- 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
- ATP, PO4
- Pockets
- 12 · best druggability 0.75
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 | 35% helix, 27% strand | P0AA04 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- HEZ · Hexane-1,6-diol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.75 | 0.79 | 86 | HEZ, PO4 |
| 2 | 575 | 0.70 | 0.79 | 67 | ATP, HEZ |
| 3 | 360 | 0.66 | 0.81 | 42 | HEZ |
| 4 | 72 | 0.55 | 0.87 | 19 | empty |
| 5 | 170 | 0.54 | 0.79 | 21 | ATP |
Interfaces
3 interfaces between chains.
- A–C · 756 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 720 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YA1 · crystal structure of LsrK-HPr complex with ATP · 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 5YA1 · PDBe 5YA1 · UniProt P77432 · UniProt P0AA04
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