Research workbench
Crystal structure of the receiver domain of ntrx from brucella abortus
Analyse Crystal structure of the receiver domain of ntrx from brucella abortus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D6X
- Type
- protein
- Length
- 478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial regulatory, fis family protein
- UniProt
- Q2YPW6
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacterial regulatory, fis family protein | protein | 120 | 47% helix, 18% strand | Q2YPW6 |
| C, D | Bacterial regulatory, fis family protein | protein | 119 | 45% helix, 18% strand | Q2YPW6 |
Ligands and binding sites
- IMD · Imidazole · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.65 | 0.78 | 59 | IMD |
| 2 | 103 | 0.45 | 0.79 | 17 | IMD |
Interfaces
4 interfaces between chains.
- B–C · 511 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 474 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 432 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4D6X · Crystal structure of the receiver domain of NtrX from Brucella abortus · 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 Q2YPW6
- Elsewhere: RCSB PDB 4D6X · PDBe 4D6X · UniProt Q2YPW6
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