Research workbench
Crystal structures of full-length fixj from B. japonicum crystallized in space group P212121
Analyse Crystal structures of full-length fixj from B. japonicum crystallized in space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XT2
- Type
- protein
- Length
- 1,015 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator fixj
- UniProt
- A0A0M9B7W0
- Ligands
- MG
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Response regulator fixj | protein | 202 | 60% helix, 13% strand | A0A0M9B7W0 |
| B, C | Response regulator fixj | protein | 204 | 58% helix, 12% strand | A0A0M9B7W0 |
| E | Response regulator fixj | protein | 203 | 55% helix, 14% strand | A0A0M9B7W0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 8 copies · chains A, C, D
- FMT · Formic acid · additive · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.63 | 0.75 | 56 | MG |
| 2 | 161 | 0.48 | 0.77 | 18 | empty |
| 3 | 155 | 0.47 | 0.77 | 31 | empty |
| 4 | 117 | 0.45 | 0.78 | 25 | FMT |
| 5 | 69 | 0.33 | 0.76 | 17 | empty |
Interfaces
7 interfaces between chains.
- B–D · 942 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 904 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 571 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 346 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 272 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5XT2 · Crystal structures of full-length FixJ from B. japonicum crystallized in space group… · 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 A0A0M9B7W0
- Elsewhere: RCSB PDB 5XT2 · PDBe 5XT2 · UniProt A0A0M9B7W0
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