MolNFT v1 · #172878 · protein
High-resolution structure of the K+/H+ antiporter subunit khtt in complex with C-di-AMP
7AGV · K(+)/H(+) antiporter subunit khtt: “High-resolution structure of the K+/H+ antiporter subunit khtt in complex with C-di-AMP”. X-ray diffraction, 2 ligands (2BA, CA), 20 pockets (best druggability 0.86). MolNFT v1 #172878 on…
- PDB
- 7AGV
- Type
- protein
- Length
- 1,287 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K(+)/H(+) antiporter subunit khtt
- UniProt
- O07535
- Ligands
- 2BA, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | K(+)/H(+) antiporter subunit khtt | protein | 160 | 18% helix, 38% strand | O07535 |
| B, E | K(+)/H(+) antiporter subunit khtt | protein | 161 | 19% helix, 40% strand | O07535 |
| D | K(+)/H(+) antiporter subunit khtt | protein | 160 | 19% helix, 38% strand | O07535 |
| F | K(+)/H(+) antiporter subunit khtt | protein | 163 | 20% helix, 37% strand | O07535 |
| H | K(+)/H(+) antiporter subunit khtt | protein | 162 | 19% helix, 40% strand | O07535 |
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 · 4 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 2 copies · chains A, G
- ACT · Acetate ion · additive · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.86 | 0.87 | 99 | ACT |
| 2 | 971 | 0.84 | 0.85 | 78 | ACT |
| 3 | 1151 | 0.84 | 0.84 | 94 | ACT |
| 4 | 977 | 0.82 | 0.83 | 77 | ACT |
| 5 | 80 | 0.77 | 0.99 | 21 | ACT |
Interfaces
11 interfaces between chains.
- G–H · 2784 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2780 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2698 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2685 Ų buried · 27 hydrogen bonds · protein-protein
- C–G · 810 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7AGV · High-resolution structure of the K+/H+ antiporter subunit KhtT in complex with c-di-AMP · the same entry in another collection · chain H against H, TM-score 1.00
- O07535 · AlphaFold monomer V2.0 prediction for K(+)/H(+) antiporter subunit khtt (O07535) · a predicted model of the same protein · chain H against A, TM-score 0.51
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 O07535
- Elsewhere: RCSB PDB 7AGV · PDBe 7AGV · UniProt O07535
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