Research workbench
Crystal structure of TETX2 T280A: an adaptive mutant in complex with minocycline
Analyse Crystal structure of TETX2 T280A: an adaptive mutant in complex with minocycline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V3N
- Type
- protein
- Length
- 1,470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TETX2 protein
- UniProt
- Q93L51
- Ligands
- MIY, FAD, SO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TETX2 protein | protein | 367 | 32% helix, 26% strand | Q93L51 |
| B, C | TETX2 protein | protein | 368 | 32% helix, 26% strand | Q93L51 |
| D | TETX2 protein | protein | 367 | 32% helix, 25% strand | Q93L51 |
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 · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.80 | 0.81 | 88 | MIY, FAD |
| 2 | 1001 | 0.79 | 0.81 | 98 | empty |
| 3 | 890 | 0.79 | 0.82 | 65 | MIY, FAD |
| 4 | 1146 | 0.78 | 0.80 | 90 | MIY, FAD |
| 5 | 1178 | 0.77 | 0.79 | 93 | MIY, FAD |
Interfaces
4 interfaces between chains.
- A–B · 903 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 479 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3V3N · Crystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline · the same entry in another collection · chain A against A, TM-score 1.00
- Q93L51 · AlphaFold monomer V2.0 prediction for flavin-dependent monooxygenase (Q93L51) · a predicted model of the same protein · chain D 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 Q93L51
- Elsewhere: RCSB PDB 3V3N · PDBe 3V3N · UniProt Q93L51
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