Research workbench
Ancient vana
Analyse Ancient vana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SE7
- Type
- protein
- Length
- 1,972 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vana
- Ligands
- ATP, MG
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Vana | protein | 327 | 29% helix, 30% strand | — |
| B | Vana | protein | 329 | 29% helix, 29% strand | — |
| C, E | Vana | protein | 331 | 28% helix, 30% strand | — |
| D | Vana | protein | 327 | 26% helix, 31% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.80 | 0.82 | 92 | empty |
| 2 | 328 | 0.72 | 0.85 | 51 | ATP, MG |
| 3 | 332 | 0.72 | 0.85 | 49 | ATP, MG |
| 4 | 310 | 0.72 | 0.85 | 50 | ATP, MG |
| 5 | 288 | 0.72 | 0.86 | 50 | ATP, MG |
Interfaces
9 interfaces between chains.
- C–D · 1594 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1558 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1541 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 217 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 160 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SE7 · ancient VanA · 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 3SE7 · PDBe 3SE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.