Research workbench
Vchtnsc aaa+ ATPase with DNA, single heptamer
Analyse Vchtnsc aaa+ ATPase with DNA, single heptamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UFI
- Type
- protein + DNA
- Length
- 2,219 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*CP*TP*CP*CP*AP*GP*TP*AP*CP*AP*GP*CP*GP*CP*GP*GP*CP*TP*GP*AP*A)- 3'); DNA…
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 47% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(P*CP*TP*CP*CP*AP*GP*TP*AP*CP*AP*GP*CP*GP*CP*GP*GP*CP*TP*GP*AP*A)- 3') | dna | 21 | — | — |
| B | DNA (5'- D(P*TP*TP*CP*AP*GP*CP*CP*GP*CP*GP*CP*TP*GP*TP*AP*CP*TP*GP*GP*AP*G)- 3') | dna | 21 | — | — |
| 1, 2, 3, 4, 5, 6, 7 | Vchtnsc | protein | 311 | 47% helix, 6% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains 1, 7, 2, 3, 4, 5, 6
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 | 1012 | 0.85 | 0.86 | 107 | ATP |
| 2 | 629 | 0.83 | 0.88 | 83 | ATP |
| 3 | 331 | 0.78 | 0.89 | 50 | ATP |
| 4 | 423 | 0.78 | 0.87 | 49 | empty |
| 5 | 303 | 0.78 | 0.89 | 45 | ATP |
Interfaces
20 interfaces between chains.
- 1–7 · 1513 Ų buried · 31 hydrogen bonds · protein-protein
- 3–4 · 1499 Ų buried · 34 hydrogen bonds · protein-protein
- 6–7 · 1492 Ų buried · 26 hydrogen bonds · protein-protein
- 2–3 · 1443 Ų buried · 24 hydrogen bonds · protein-protein
- 1–2 · 1432 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7UFI · VchTnsC AAA+ ATPase with DNA, single heptamer · the same entry in another collection · chain 5 against 5, 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 7UFI · PDBe 7UFI
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