Research workbench
Crystal structure of a putative hth-type transcriptional regulator ytcd
Analyse Crystal structure of a putative hth-type transcriptional regulator ytcd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HZT
- Type
- protein
- Length
- 386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hth-type transcriptional regulator ytcd
- UniProt
- O34533
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative hth-type transcriptional regulator ytcd | protein | 98 | 57% helix, 13% strand | O34533 |
| C, D | Putative hth-type transcriptional regulator ytcd | protein | 95 | 60% helix, 13% strand | O34533 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.67 | 0.77 | 53 | empty |
| 2 | 173 | 0.56 | 0.80 | 27 | empty |
| 3 | 60 | 0.29 | 0.74 | 17 | empty |
| 4 | 51 | 0.27 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1501 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1478 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 163 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered, nonstandard).
Compared structures
- 2HZT · Crystal Structure of a putative HTH-type transcriptional regulator ytcD · the same entry in another collection · chain A against A, TM-score 1.00
- O34533 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain C against A, TM-score 0.94
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 O34533
- Elsewhere: RCSB PDB 2HZT · PDBe 2HZT · UniProt O34533
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