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Low-resolution structure of the K+/H+ antiporter subunit khtt in complex with C-di-AMP
Analyse Low-resolution structure of the K+/H+ antiporter subunit khtt in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AHM
- Type
- protein
- Length
- 647 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K(+)/H(+) antiporter subunit khtt
- UniProt
- O07535
- Ligands
- 2BA
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K(+)/H(+) antiporter subunit khtt | protein | 162 | 24% helix, 36% strand | O07535 |
| B | K(+)/H(+) antiporter subunit khtt | protein | 163 | 19% helix, 34% strand | O07535 |
| C | K(+)/H(+) antiporter subunit khtt | protein | 161 | 21% helix, 30% strand | O07535 |
| D | K(+)/H(+) antiporter subunit khtt | protein | 161 | 20% helix, 29% 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 · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.74 | 1.00 | 19 | empty |
| 2 | 642 | 0.70 | 0.78 | 59 | empty |
| 3 | 317 | 0.67 | 0.82 | 24 | 2BA |
| 4 | 241 | 0.63 | 0.82 | 25 | 2BA |
| 5 | 406 | 0.61 | 0.77 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3001 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2858 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 934 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 191 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7AHM · Low-resolution structure of the K+/H+ antiporter subunit KhtT in complex with c-di-AMP · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.55
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 7AHM · PDBe 7AHM · UniProt O07535
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