Research workbench
Nachbac in gdn
Analyse Nachbac in gdn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VX3
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BH1501 protein
- UniProt
- Q9KCR8
- Ligands
- POV
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | BH1501 protein | protein | 225 | 64% helix, 0% strand | Q9KCR8 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 8 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.82 | 0.83 | 93 | empty |
| 2 | 86 | 0.55 | 0.85 | 16 | empty |
| 3 | 142 | 0.50 | 0.79 | 28 | empty |
| 4 | 120 | 0.47 | 0.78 | 22 | empty |
| 5 | 120 | 0.47 | 0.79 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1672 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 1671 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1666 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1658 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6VX3 · NaChBac in GDN · the same entry in another collection · chain C against C, 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
- Every structure of UniProt Q9KCR8
- Elsewhere: RCSB PDB 6VX3 · PDBe 6VX3 · UniProt Q9KCR8
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