Research workbench
Crystal structure of the putative phosphohistidine phosphatase sixa from agrobacterium tumefaciens
Analyse Crystal structure of the putative phosphohistidine phosphatase sixa from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RFL
- Type
- protein
- Length
- 1,212 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphohistidine phosphatase sixa
- EC
- 5.4.2.1, 3.1.3.13, 5.4.2.4
- UniProt
- Q8UFN9
- Ligands
- SCN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 149 | 40% helix, 22% strand | Q8UFN9 |
| B | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 154 | 40% helix, 23% strand | Q8UFN9 |
| C | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 151 | 40% helix, 22% strand | Q8UFN9 |
| D | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 147 | 35% helix, 22% strand | Q8UFN9 |
| E | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 154 | 40% helix, 23% strand | Q8UFN9 |
| F | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 147 | 37% helix, 24% strand | Q8UFN9 |
| G | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 154 | 40% helix, 23% strand | Q8UFN9 |
| H | Putative phosphohistidine phosphatase sixa (EC 5.4.2.1, 3.1.3.13, 5.4.2.4) | protein | 156 | 37% helix, 22% strand | Q8UFN9 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion
- GOL · Glycerol · additive · 2 copies · chains G
- ACY · Acetic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.81 | 0.84 | 92 | empty |
| 2 | 650 | 0.81 | 0.86 | 87 | empty |
| 3 | 1039 | 0.74 | 0.77 | 129 | empty |
| 4 | 292 | 0.59 | 0.78 | 46 | empty |
| 5 | 287 | 0.58 | 0.78 | 40 | empty |
Interfaces
14 interfaces between chains.
- A–E · 795 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 790 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 789 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 777 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 771 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2RFL · Crystal structure of the putative phosphohistidine phosphatase SixA from Agrobacterium… · 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 Q8UFN9
- Elsewhere: RCSB PDB 2RFL · PDBe 2RFL · UniProt Q8UFN9
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