Research workbench
MDT PROTEIN
Analyse MDT PROTEIN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DNV
- Type
- protein + DNA
- Length
- 506 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hipa; Hth-type transcriptional regulator hipb; DNA (5'…
- UniProt
- P23874, P23873
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein hipa | protein | 414 | 37% helix, 20% strand | P23874 |
| B | Hth-type transcriptional regulator hipb | protein | 71 | 62% helix, 0% strand | P23873 |
| T | DNA (5'- D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DG P*DAP*DTP*DAP*DG)-3') | dna | 21 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.79 | 0.97 | 29 | empty |
| 2 | 114 | 0.67 | 0.90 | 25 | empty |
| 3 | 570 | 0.66 | 0.76 | 66 | empty |
| 4 | 102 | 0.63 | 0.88 | 27 | empty |
| 5 | 115 | 0.49 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 547 Ų buried · 5 hydrogen bonds · protein-protein
- B–T · 314 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–T · 111 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3DNV · MDT Protein · the same entry in another collection · chain B against B, 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 3DNV · PDBe 3DNV · UniProt P23874 · UniProt P23873
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