MolNFT v1 · #115468 · protein
Crystal structure of kora, a plasmid-encoded, global transcription regulator
5CKT · Trfb transcriptional repressor protein: “Crystal structure of kora, a plasmid-encoded, global transcription regulator”. X-ray diffraction, 8 pockets (best druggability 0.69). MolNFT v1 #115468 on GenesisL1: 3D structure, binding…
- PDB
- 5CKT
- Type
- protein
- Length
- 391 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trfb transcriptional repressor protein
- UniProt
- P03052
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Trfb transcriptional repressor protein | protein | 99 | 65% helix, 9% strand | P03052 |
| D | Trfb transcriptional repressor protein | protein | 94 | 67% helix, 10% strand | P03052 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, 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 | 794 | 0.69 | 0.76 | 69 | ACT |
| 2 | 193 | 0.48 | 0.75 | 18 | empty |
| 3 | 178 | 0.48 | 0.76 | 20 | empty |
| 4 | 117 | 0.47 | 0.79 | 20 | empty |
| 5 | 181 | 0.44 | 0.74 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1496 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1259 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 414 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 255 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 120 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5CKT · Crystal Structure of KorA, a plasmid-encoded, global transcription regulator · the same entry in another collection · chain A against A, TM-score 1.00
- P03052 · AlphaFold monomer V2.0 prediction for trfb transcriptional repressor protein (P03052) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P03052
- Elsewhere: RCSB PDB 5CKT · PDBe 5CKT · UniProt P03052
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