Research workbench
The structure of protozoan parasite trichomonas vaginalis MYB2 in complex with mre-2F-13 DNA
Analyse The structure of protozoan parasite trichomonas vaginalis MYB2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OSF
- Type
- protein + DNA
- Length
- 258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MYB21; 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3'…
- UniProt
- Q58HP3
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MYB21 | protein | 103 | 62% helix, 0% strand | Q58HP3 |
| B, E | 5'-D(*CP*TP*GP*TP*AP*TP*CP*GP*TP*CP*TP*TP*G)-3' | dna | 13 | — | — |
| C, F | 5'-D(*CP*AP*AP*GP*AP*CP*GP*AP*TP*AP*CP*AP*G)-3' | dna | 13 | — | — |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.64 | 0.93 | 21 | empty |
| 2 | 110 | 0.58 | 0.86 | 25 | empty |
| 3 | 87 | 0.42 | 0.79 | 16 | empty |
| 4 | 119 | 0.40 | 0.76 | 17 | empty |
| 5 | 77 | 0.38 | 0.78 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–F · 719 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 681 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 670 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 629 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- D–E · 609 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3OSF · The structure of protozoan parasite Trichomonas vaginalis Myb2 in complex with MRE-2f-13… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q58HP3
- Elsewhere: RCSB PDB 3OSF · PDBe 3OSF · UniProt Q58HP3
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