MolNFT v1 · #22893 · protein
Crystal structure of transcription factor dksa from E. COLI
1TJL · Dnak suppressor protein: “Crystal structure of transcription factor dksa from E. COLI”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.66). MolNFT v1 #22893 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1TJL
- Type
- protein
- Length
- 1,450 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnak suppressor protein
- UniProt
- P0ABS1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Dnak suppressor protein | protein | 145 | 66% helix, 1% strand | P0ABS1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.66 | 0.75 | 72 | empty |
| 2 | 474 | 0.65 | 0.77 | 41 | empty |
| 3 | 222 | 0.63 | 0.82 | 38 | empty |
| 4 | 344 | 0.59 | 0.77 | 33 | empty |
| 5 | 211 | 0.57 | 0.79 | 21 | empty |
Interfaces
17 interfaces between chains.
- A–C · 1067 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 974 Ų buried · 10 hydrogen bonds · protein-protein
- B–J · 956 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 794 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 785 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1TJL · Crystal structure of transcription factor DksA from E. coli · the same entry in another collection · chain J against J, TM-score 1.00
- P0ABS1 · AlphaFold monomer V2.0 prediction for RNA polymerase-binding transcription factor dksa… · a predicted model of the same protein · chain J against A, TM-score 0.96
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 P0ABS1
- Elsewhere: RCSB PDB 1TJL · PDBe 1TJL · UniProt P0ABS1
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