Research workbench
Crystal structure of the sodium binding rotor ring at pH 8.7
Analyse Crystal structure of the sodium binding rotor ring at pH 8.7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZK2
- Type
- protein
- Length
- 1,958 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit C
- UniProt
- Q8RGD7
- Ligands
- NA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V | ATP synthase subunit C | protein | 89 | 91% helix, 0% strand | Q8RGD7 |
Ligands and binding sites
- NA · Sodium ion · metal · 22 copies · chains A, K, B, C, D, E, F, G, H, I, J, L, V, M, N, O, P, Q, R, S, T, U
- DMU · Decyl-beta-D-maltopyranoside · additive · 23 copies · chains A, B, C, K, D, E, F, G, H, I, J, L, M, N, O, P, Q, R, S, T, U, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.79 | 0.79 | 68 | empty |
| 2 | 1068 | 0.78 | 0.79 | 76 | empty |
| 3 | 246 | 0.55 | 0.77 | 34 | empty |
| 4 | 117 | 0.42 | 0.76 | 21 | empty |
Interfaces
26 interfaces between chains.
- E–F · 1967 Ų buried · 11 hydrogen bonds · protein-protein
- A–K · 1960 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 1955 Ų buried · 10 hydrogen bonds · protein-protein
- P–Q · 1952 Ų buried · 11 hydrogen bonds · protein-protein
- L–V · 1952 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3ZK2 · Crystal structure of the sodium binding rotor ring at pH 8.7 · the same entry in another collection · chain P against P, 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 Q8RGD7
- Elsewhere: RCSB PDB 3ZK2 · PDBe 3ZK2 · UniProt Q8RGD7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.