Research workbench
Cryo-EM structure of E. COLI tnsb in complex with right end fragment of TN7 transposon
Analyse Cryo-EM structure of E. COLI tnsb in complex with right end fragment of TN7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PIK
- Type
- protein + DNA
- Length
- 1,750 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposon TN7 transposition protein tnsb; Right end fragment of TN7 transposon
- UniProt
- P13989
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 7 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposon TN7 transposition protein tnsb | protein | 151 | 42% helix, 18% strand | P13989 |
| B | Transposon TN7 transposition protein tnsb | protein | 541 | 36% helix, 17% strand | P13989 |
| C | Transposon TN7 transposition protein tnsb | protein | 557 | 43% helix, 17% strand | P13989 |
| D | Transposon TN7 transposition protein tnsb | protein | 335 | 35% helix, 20% strand | P13989 |
| K | Right end fragment of TN7 transposon | dna | 63 | — | — |
| L | Right end fragment of TN7 transposon | dna | 63 | — | — |
| E | Transposon TN7 transposition protein tnsb | protein | 40 | 88% helix, 0% strand | P13989 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.73 | 0.78 | 75 | empty |
| 2 | 563 | 0.71 | 0.80 | 54 | empty |
| 3 | 210 | 0.69 | 0.87 | 28 | empty |
| 4 | 445 | 0.65 | 0.78 | 46 | empty |
| 5 | 443 | 0.64 | 0.77 | 39 | empty |
Interfaces
13 interfaces between chains.
- K–L · 2769 Ų buried · 230 hydrogen bonds · nucleic-nucleic
- C–D · 1538 Ų buried · 12 hydrogen bonds · protein-protein
- B–K · 1343 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 1343 Ų buried · 2 hydrogen bonds · protein-protein
- C–K · 1143 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 7PIK · Cryo-EM structure of E. coli TnsB in complex with right end fragment of Tn7 transposon · the same entry in another collection · chain E against E, TM-score 1.00
- P13989 · AlphaFold monomer V2.0 prediction for transposon TN7 transposition protein tnsb (P13989) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P13989
- Elsewhere: RCSB PDB 7PIK · PDBe 7PIK · UniProt P13989
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