Research workbench
Vchtnsc aaa+ with DNA (double heptamer)
Analyse Vchtnsc aaa+ with DNA (double heptamer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UFM
- Type
- protein + DNA
- Length
- 4,426 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vchtnsc; DNA (36-mer)
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 45% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Vchtnsc | protein | 311 | 45% helix, 5% strand | — |
| O | DNA (36-mer) | dna | 36 | — | — |
| P | DNA (36-mer) | dna | 36 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 714 | 0.82 | 0.86 | 79 | ATP |
| 2 | 701 | 0.82 | 0.86 | 89 | ATP |
| 3 | 678 | 0.81 | 0.86 | 72 | empty |
| 4 | 864 | 0.81 | 0.84 | 84 | ATP |
| 5 | 769 | 0.81 | 0.84 | 81 | ATP |
Interfaces
45 interfaces between chains.
- O–P · 1614 Ų buried · 204 hydrogen bonds · nucleic-nucleic
- K–L · 1540 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1517 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 1514 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1514 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7UFM · VchTnsC AAA+ with DNA (double heptamer) · 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 7UFM · PDBe 7UFM
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