Research workbench
X-ray structure of brucella abortus rica
Analyse X-ray structure of brucella abortus rica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N27
- Type
- protein
- Length
- 1,050 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial transferase hexapeptide repeat
- UniProt
- Q2YQG1
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Bacterial transferase hexapeptide repeat | protein | 175 | 14% helix, 39% strand | Q2YQG1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 6 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.78 | 0.80 | 135 | PE5, ZN |
| 2 | 581 | 0.72 | 0.80 | 63 | PE5, ZN |
| 3 | 638 | 0.68 | 0.77 | 55 | ZN, PE5 |
| 4 | 417 | 0.63 | 0.77 | 47 | PE5 |
| 5 | 144 | 0.53 | 0.81 | 29 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1033 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1022 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1018 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1013 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1006 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4N27 · X-ray structure of Brucella abortus RicA · 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 Q2YQG1
- Elsewhere: RCSB PDB 4N27 · PDBe 4N27 · UniProt Q2YQG1
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