Research workbench
Structure of mdt protein
Analyse Structure of mdt protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HZI
- Type
- protein + DNA
- Length
- 515 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hipa; Hth-type transcriptional regulator hipb…
- UniProt
- P23874, P23873
- Ligands
- ATP, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein hipa | protein | 423 | 33% helix, 18% strand | P23874 |
| B | Hth-type transcriptional regulator hipb | protein | 71 | 54% helix, 0% strand | P23873 |
| T | 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*D GP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3' | dna | 21 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.81 | 0.91 | 50 | ATP |
| 2 | 628 | 0.67 | 0.76 | 73 | empty |
| 3 | 111 | 0.57 | 0.84 | 23 | empty |
| 4 | 81 | 0.40 | 0.78 | 16 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 483 Ų buried · 3 hydrogen bonds · protein-protein
- B–T · 311 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–T · 81 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3HZI · Structure of mdt protein · the same entry in another collection · chain A against A, TM-score 1.00
- P23874 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase toxin hipa (P23874) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P23873 · AlphaFold monomer V2.0 prediction for antitoxin hipb (P23873) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P23874
- Every structure of UniProt P23873
- Elsewhere: RCSB PDB 3HZI · PDBe 3HZI · UniProt P23874 · UniProt P23873
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