MolNFT v1 · #50113 · protein
Crystal structure of the N-terminal region (19..243) of sensor protein kdpd from pseudomonas syringae pv. tomato str. DC3000
2R8R: “Crystal structure of the N-terminal region (19..243) of sensor protein kdpd from pseudomonas syringae pv.…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.88). MolNFT v1 #50113 on GenesisL1: 3D structure, binding…
- PDB
- 2R8R
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor protein
- EC
- 2.7.13.3
- UniProt
- Q883V3
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor protein (EC 2.7.13.3) | protein | 209 | 43% helix, 20% strand | Q883V3 |
| B | Sensor protein (EC 2.7.13.3) | protein | 207 | 44% helix, 19% strand | Q883V3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.88 | 0.89 | 126 | SO4 |
| 2 | 83 | 0.36 | 0.76 | 15 | empty |
| 3 | 51 | 0.34 | 0.79 | 18 | empty |
| 4 | 80 | 0.32 | 0.74 | 19 | empty |
| 5 | 57 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2R8R · Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q883V3
- Elsewhere: RCSB PDB 2R8R · PDBe 2R8R · UniProt Q883V3
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