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High-resolution structure of the K+/H+ antiporter subunit khtt in complex with C-di-AMP

Analyse High-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: 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.

Pocket	Volume (Å³)	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 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2780 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2698 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2685 Å² buried · 27 hydrogen bonds · protein-protein
C–G · 810 Å² 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

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Every structure of UniProt O07535
Elsewhere: RCSB PDB 7AGV · PDBe 7AGV · UniProt O07535

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