MolNFT v1 · #118453 · protein
Structure of rck domain with cda
5F29 · NA+/H+ antiporter-like protein: “Structure of rck domain with cda”. X-ray diffraction, 1 ligand (2BA), 1 pocket (best druggability 0.54). MolNFT v1 #118453 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F29
- Type
- protein
- Length
- 141 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA+/H+ antiporter-like protein
- UniProt
- A0A077VS08
- Ligands
- 2BA
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA+/H+ antiporter-like protein | protein | 70 | 24% helix, 33% strand | A0A077VS08 |
| B | NA+/H+ antiporter-like protein | protein | 71 | 25% helix, 32% strand | A0A077VS08 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.54 | 0.78 | 19 | 2BA |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 5F29 · Structure of RCK domain with cda · 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 A0A077VS08
- Elsewhere: RCSB PDB 5F29 · PDBe 5F29 · UniProt A0A077VS08
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.