Research workbench
Scytonema hofmannii tnsc bound to amppnp and DNA
Analyse Scytonema hofmannii tnsc bound to amppnp and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PLH
- Type
- protein + DNA
- Length
- 1,864 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shtnsc; DNA (5'- D(P*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)…
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Shtnsc | protein | 260 | 54% helix, 8% strand | — |
| H, I | DNA (5'- D(P*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T) -3') | dna | 22 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 7 copies · chains A, B, C, D, E, F, G
- MG · Magnesium ion · metal · 7 copies · chains A, 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 | 446 | 0.81 | 0.89 | 55 | empty |
| 2 | 492 | 0.79 | 0.87 | 50 | ANP, MG |
| 3 | 534 | 0.78 | 0.85 | 58 | ANP, MG |
| 4 | 468 | 0.78 | 0.86 | 50 | ANP, MG |
| 5 | 329 | 0.78 | 0.89 | 56 | empty |
Interfaces
24 interfaces between chains.
- C–D · 1191 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1169 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1164 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1128 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1117 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7PLH · Scytonema hofmannii TnsC bound to AMPPNP and DNA · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 7PLH · PDBe 7PLH
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