MolNFT v1 · #54468 · protein
TETR(D) in complex with minocycline and magnesium.
2XPV · Tetracycline repressor protein class D: “TETR(D) in complex with minocycline and magnesium.”. X-ray diffraction, 3 ligands (MIY, MG, CL), 2 pockets (best druggability 0.63). MolNFT v1 #54468 on GenesisL1: 3D structure, binding sites…
- PDB
- 2XPV
- Type
- protein
- Length
- 199 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetracycline repressor protein class D
- UniProt
- P0ACT4
- Ligands
- MIY, MG, CL
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetracycline repressor protein class D | protein | 199 | 74% helix, 0% strand | P0ACT4 |
Ligands and binding sites
- MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.63 | 0.81 | 27 | MIY, MG |
| 2 | 51 | 0.31 | 0.76 | 12 | empty |
Compared structures
- 2XPV · TetR(D) in complex with minocycline and magnesium. · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACT4 · AlphaFold monomer V2.0 prediction for tetracycline repressor protein class D (P0ACT4) · 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 P0ACT4
- Elsewhere: RCSB PDB 2XPV · PDBe 2XPV · UniProt P0ACT4
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