MolNFT v1 · #115513 · protein + DNA
Crystal structure of kora, a plasmid-encoded, global transcription regulator
5CM3 · Trfb transcriptional repressor protein: “Crystal structure of kora, a plasmid-encoded, global transcription regulator”. X-ray diffraction, 3 pockets (best druggability 0.52). MolNFT v1 #115513 on GenesisL1: 3D structure, binding…
- PDB
- 5CM3
- Type
- protein + DNA
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trfb transcriptional repressor protein; 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*…
- UniProt
- P03052
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trfb transcriptional repressor protein | protein | 97 | 63% helix, 8% strand | P03052 |
| B | Trfb transcriptional repressor protein | protein | 93 | 62% helix, 9% strand | P03052 |
| C, D | 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP* GP*GP*)-3' | dna | 19 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.52 | 0.75 | 32 | empty |
| 2 | 117 | 0.43 | 0.77 | 19 | empty |
| 3 | 125 | 0.42 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1087 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 808 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–C · 486 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 444 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 379 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 5CM3 · 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 0.83
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 5CM3 · PDBe 5CM3 · UniProt P03052
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