MolNFT v1 · #12561 · protein
L.CASEI HPRK/P in complex with B.SUBTILIS hpr
1KKL · Hprk protein: “L.CASEI HPRK/P in complex with B.SUBTILIS hpr”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.67). MolNFT v1 #12561 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KKL
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hprk protein; Phosphocarrier protein hpr
- EC
- 2.7.1.-, 3.1.3.-
- UniProt
- Q9RE09, P08877
- Ligands
- CA
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hprk protein (EC 2.7.1.-, 3.1.3.-) | protein | 167 | 32% helix, 40% strand | Q9RE09 |
| B | Hprk protein (EC 2.7.1.-, 3.1.3.-) | protein | 166 | 30% helix, 39% strand | Q9RE09 |
| C | Hprk protein (EC 2.7.1.-, 3.1.3.-) | protein | 168 | 32% helix, 41% strand | Q9RE09 |
| H | Phosphocarrier protein hpr | protein | 86 | 37% helix, 27% strand | P08877 |
| I | Phosphocarrier protein hpr | protein | 87 | 37% helix, 28% strand | P08877 |
| J | Phosphocarrier protein hpr | protein | 88 | 35% helix, 28% strand | P08877 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.67 | 0.77 | 61 | CA |
| 2 | 403 | 0.62 | 0.77 | 55 | CA |
| 3 | 370 | 0.61 | 0.77 | 50 | CA |
| 4 | 116 | 0.38 | 0.74 | 23 | empty |
| 5 | 114 | 0.37 | 0.74 | 21 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1039 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1037 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1035 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 529 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 522 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1KKL · L.casei HprK/P in complex with B.subtilis HPr · the same entry in another collection · chain J against J, TM-score 1.00
- Q9RE09 · AlphaFold monomer V2.0 prediction for hpr KINASE/PHOSPHORYLASE (Q9RE09) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P08877 · AlphaFold monomer V2.0 prediction for phosphocarrier protein hpr (P08877) · a predicted model of the same protein · chain I against A, TM-score 0.98
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 Q9RE09
- Every structure of UniProt P08877
- Elsewhere: RCSB PDB 1KKL · PDBe 1KKL · UniProt Q9RE09 · UniProt P08877
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