MolNFT v1 · #12562 · protein
L.CASEI HPRK/P in complex with B.SUBTILIS P-ser-hpr
1KKM · Hprk protein: “L.CASEI HPRK/P in complex with B.SUBTILIS P-ser-hpr”. X-ray diffraction, 2 ligands (CA, PO4), 7 pockets (best druggability 0.73). MolNFT v1 #12562 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KKM
- Type
- protein
- Length
- 789 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, PO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hprk protein (EC 2.7.1.-, 3.1.3.-) | protein | 176 | 30% helix, 39% strand | Q9RE09 |
| B | Hprk protein (EC 2.7.1.-, 3.1.3.-) | protein | 177 | 30% helix, 40% strand | Q9RE09 |
| C | Hprk protein (EC 2.7.1.-, 3.1.3.-) | protein | 175 | 30% helix, 38% strand | Q9RE09 |
| H, I, J | Phosphocarrier protein hpr | protein | 87 | 38% helix, 28% strand | P08877 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C, H, B, I, J
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, H, B, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.73 | 0.97 | 34 | empty |
| 2 | 410 | 0.69 | 0.81 | 53 | CA, PO4 |
| 3 | 426 | 0.68 | 0.81 | 61 | CA, PO4 |
| 4 | 417 | 0.68 | 0.80 | 63 | PO4 |
| 5 | 57 | 0.47 | 0.85 | 19 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1228 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1216 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1202 Ų buried · 6 hydrogen bonds · protein-protein
- B–J · 610 Ų buried · 7 hydrogen bonds · protein-protein
- A–I · 603 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 1KKM · L.casei HprK/P in complex with B.subtilis P-Ser-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 A 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 H against A, TM-score 0.97
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 1KKM · PDBe 1KKM · UniProt Q9RE09 · UniProt P08877
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