Research workbench
Tnsbctd-tnsc complex
Analyse Tnsbctd-tnsc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SVV
- Type
- protein + DNA
- Length
- 2,748 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); DNA (5'…
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 19 | — | — |
| 2 | DNA (5'- D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 19 | — | — |
| A, B, C, D, E, F, G, H, I, J | Tnsc filament | protein | 257 | 54% helix, 11% strand | — |
| a, b, c, d, e, f, g, h, i, j | Tnsbctd | protein | 14 | 43% helix, 14% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
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 | 1177 | 0.82 | 0.83 | 126 | ANP, MG |
| 2 | 666 | 0.81 | 0.85 | 61 | ANP, MG |
| 3 | 885 | 0.81 | 0.83 | 75 | ANP, MG |
| 4 | 873 | 0.80 | 0.82 | 76 | ANP, MG |
| 5 | 854 | 0.80 | 0.82 | 77 | ANP, MG |
Interfaces
48 interfaces between chains.
- D–E · 1046 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1046 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1045 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1045 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1044 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7SVV · TnsBctd-TnsC complex · the same entry in another collection · chain 1 against 1, 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 7SVV · PDBe 7SVV
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