MolNFT v1 · #22273 · protein
Crystal structure of the TNSA/TNSC(504-555) complex
1T0F · Transposon TN7 transposition protein tnsa: “Crystal structure of the TNSA/TNSC(504-555) complex”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.76). MolNFT v1 #22273 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1T0F
- Type
- protein
- Length
- 622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposon TN7 transposition protein tnsa; Transposon TN7 transposition protein tnsc
- UniProt
- P13988, P05846
- Ligands
- MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposon TN7 transposition protein tnsa | protein | 264 | 44% helix, 18% strand | P13988 |
| B | Transposon TN7 transposition protein tnsa | protein | 262 | 45% helix, 18% strand | P13988 |
| C | Transposon TN7 transposition protein tnsc | protein | 49 | 47% helix, 2% strand | P05846 |
| D | Transposon TN7 transposition protein tnsc | protein | 47 | 49% helix, 2% strand | P05846 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
- MLA · Malonic acid · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.76 | 0.78 | 125 | MPD |
| 2 | 394 | 0.66 | 0.79 | 38 | MG, MPD |
| 3 | 329 | 0.62 | 0.79 | 32 | MG |
| 4 | 107 | 0.39 | 0.75 | 21 | empty |
| 5 | 96 | 0.39 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1314 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1272 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1121 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1T0F · Crystal Structure of the TnsA/TnsC(504-555) complex · the same entry in another collection · chain D against D, TM-score 1.00
- P13988 · AlphaFold monomer V2.0 prediction for transposon TN7 transposition protein tnsa (P13988) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P05846 · AlphaFold monomer V2.0 prediction for transposon TN7 transposition protein tnsc (P05846) · a predicted model of the same protein · chain D against A, TM-score 0.77
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 P13988
- Every structure of UniProt P05846
- Elsewhere: RCSB PDB 1T0F · PDBe 1T0F · UniProt P13988 · UniProt P05846
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