Research workbench
Navab normopp mutant
Analyse Navab normopp mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C1M
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- PX4, 1N7, MGX, NA, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 230 | 79% helix, 0% strand | A8EVM5 |
| B | Ion transport protein | protein | 223 | 83% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains A, B
- 1N7 · Chapso · ligand · 8 copies · chains A, B
- MGX · 1-methylguanidine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.69 | 0.77 | 52 | PX4 |
| 2 | 268 | 0.55 | 0.77 | 30 | MGX |
| 3 | 118 | 0.49 | 0.80 | 20 | empty |
| 4 | 174 | 0.47 | 0.76 | 23 | MGX |
| 5 | 126 | 0.47 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1615 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6C1M · NavAb NormoPP mutant · 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
- Every structure of UniProt A8EVM5
- Elsewhere: RCSB PDB 6C1M · PDBe 6C1M · UniProt A8EVM5
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