Research workbench
Cryo-electron microscopy structure of TNSC(1-503)A225V bound to DNA
Analyse Cryo-electron microscopy structure of TNSC(1-503)A225V bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MCS
- Type
- protein + DNA
- Length
- 2,649 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposon TN7 transposition protein tnsc; DNA…
- UniProt
- P05846
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposon TN7 transposition protein tnsc | protein | 249 | 41% helix, 10% strand | P05846 |
| B | Transposon TN7 transposition protein tnsc | protein | 402 | 46% helix, 9% strand | P05846 |
| C | Transposon TN7 transposition protein tnsc | protein | 404 | 46% helix, 9% strand | P05846 |
| D | Transposon TN7 transposition protein tnsc | protein | 403 | 47% helix, 8% strand | P05846 |
| E | Transposon TN7 transposition protein tnsc | protein | 402 | 47% helix, 8% strand | P05846 |
| F | Transposon TN7 transposition protein tnsc | protein | 401 | 47% helix, 9% strand | P05846 |
| G | Transposon TN7 transposition protein tnsc | protein | 358 | 44% helix, 7% strand | P05846 |
| H | DNA (5'-D(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)- 3') | dna | 15 | — | — |
| I | DNA (5'-D(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)- 3') | dna | 15 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F, G
- MG · Magnesium ion · metal · 6 copies · chains B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.88 | 0.90 | 95 | ANP, MG |
| 2 | 1133 | 0.88 | 0.89 | 113 | ANP, MG |
| 3 | 1158 | 0.86 | 0.87 | 133 | ANP, MG |
| 4 | 1166 | 0.86 | 0.87 | 117 | ANP, MG |
| 5 | 999 | 0.85 | 0.86 | 95 | ANP, MG |
Interfaces
21 interfaces between chains.
- B–C · 3249 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 3149 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 3135 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3114 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3112 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7MCS · Cryo-electron microscopy structure of TnsC(1-503)A225V bound to DNA · the same entry in another collection · chain I against I, TM-score 1.00
- P05846 · AlphaFold monomer V2.0 prediction for transposon TN7 transposition protein tnsc (P05846) · a predicted model of the same protein · chain G against A, TM-score 0.90
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 P05846
- Elsewhere: RCSB PDB 7MCS · PDBe 7MCS · UniProt P05846
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