MolNFT v1 · #17135 · protein
Crystal structure of a SIGMA54-activator suggests the mechanism for the conformational switch necessary for SIGMA54 binding
1OJL · Transcriptional regulatory protein zrar: “Crystal structure of a SIGMA54-activator suggests the mechanism for the conformational switch necessary for…”. X-ray diffraction, 2 ligands (ATP, PO4), 13 pockets (best druggability 0.77).…
- PDB
- 1OJL
- Type
- protein
- Length
- 1,624 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulatory protein zrar
- UniProt
- P25852
- Ligands
- ATP, PO4
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulatory protein zrar | protein | 292 | 49% helix, 10% strand | P25852 |
| B | Transcriptional regulatory protein zrar | protein | 251 | 44% helix, 12% strand | P25852 |
| C | Transcriptional regulatory protein zrar | protein | 252 | 46% helix, 13% strand | P25852 |
| D | Transcriptional regulatory protein zrar | protein | 297 | 46% helix, 11% strand | P25852 |
| E | Transcriptional regulatory protein zrar | protein | 285 | 47% helix, 11% strand | P25852 |
| F | Transcriptional regulatory protein zrar | protein | 247 | 47% helix, 10% strand | P25852 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains E
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.77 | 0.79 | 113 | PO4 |
| 2 | 879 | 0.77 | 0.80 | 93 | PO4 |
| 3 | 1003 | 0.77 | 0.79 | 97 | ATP |
| 4 | 1012 | 0.74 | 0.77 | 103 | empty |
| 5 | 514 | 0.69 | 0.79 | 65 | PO4 |
Interfaces
7 interfaces between chains.
- B–C · 1038 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 996 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 953 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 944 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 349 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1OJL · Crystal structure of a sigma54-activator suggests the mechanism for the conformational… · the same entry in another collection · chain F against F, TM-score 1.00
- P25852 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein zrar (P25852) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P25852
- Elsewhere: RCSB PDB 1OJL · PDBe 1OJL · UniProt P25852
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