MolNFT v1 · #154735 · protein + DNA
Structural insights into target DNA recognition by R2R3-type myb transcription factor
6KKS · Transcription factor wer: “Structural insights into target DNA recognition by R2R3-type myb transcription factor”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.51). MolNFT v1 #154735 on GenesisL1: 3D structure…
- PDB
- 6KKS
- Type
- protein + DNA
- Length
- 146 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor wer; DNA (5'- D(*AP*AP*AP*TP*TP*CP*TP*CP*CP*AP*AP*CP*CP*GP*CP*AP*TP*T…
- UniProt
- Q9SEI0
- Ligands
- MG
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor wer | protein | 106 | 58% helix, 0% strand | Q9SEI0 |
| B | DNA (5'- D(*AP*AP*AP*TP*TP*CP*TP*CP*CP*AP*AP*CP*CP*GP*CP*AP*TP*TP*TP*TP*C)- 3') | dna | 19 | — | — |
| C | DNA (5'- D(*CP*GP*AP*AP*AP*AP*TP*GP*CP*GP*GP*TP*TP*GP*GP*AP*GP*AP*AP*TP*T)- 3') | dna | 21 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.51 | 0.79 | 24 | empty |
| 2 | 148 | 0.49 | 0.78 | 23 | empty |
| 3 | 201 | 0.48 | 0.76 | 17 | empty |
| 4 | 149 | 0.47 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 883 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–C · 602 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 549 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6KKS · Structural insights into target DNA recognition by R2R3-type MYB transcription factor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SEI0 · AlphaFold monomer V2.0 prediction for transcription factor wer (Q9SEI0) · a predicted model of the same protein · chain A 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 Q9SEI0
- Elsewhere: RCSB PDB 6KKS · PDBe 6KKS · UniProt Q9SEI0
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