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Structure of dimeric sodium proton antiporter nhaa, at pH 6.0, crystallized with chimeric Fab antibodies
Analyse Structure of dimeric sodium proton antiporter nhaa, at pH 6.0, crystallized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A0X
- Type
- protein
- Length
- 1,592 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA(+)/H(+) antiporter nhaa; Chimeric antibody Fab-F6, heavy CHAIN,CHIMERIC antibody…
- UniProt
- Q8ZRZ3
- Ligands
- 3PH, CDL, 3PE, CA, CL, PO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA(+)/H(+) antiporter nhaa | protein | 370 | 70% helix, 4% strand | Q8ZRZ3 |
| B | NA(+)/H(+) antiporter nhaa | protein | 373 | 72% helix, 4% strand | Q8ZRZ3 |
| C | Chimeric antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy chain | protein | 210 | 6% helix, 49% strand | — |
| D | Chimeric antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light chain | protein | 207 | 6% helix, 50% strand | — |
| E | Chimeric antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy chain | protein | 223 | 7% helix, 52% strand | — |
| F | Chimeric antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light chain | protein | 209 | 6% helix, 50% strand | — |
Ligands and binding sites
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 3 copies · chains A, B
- CDL · Cardiolipin · ligand · chains A, B
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains B
- CA · Calcium ion · metal · chains F
- CL · Chloride ion · ion · 3 copies · chains C, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, D, B, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.78 | 0.80 | 90 | PG4 |
| 2 | 969 | 0.78 | 0.80 | 83 | PG4 |
| 3 | 577 | 0.68 | 0.77 | 55 | CDL, 3PH |
| 4 | 249 | 0.64 | 0.82 | 33 | empty |
| 5 | 231 | 0.63 | 0.81 | 28 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2005 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1754 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 623 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 620 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7A0X · Structure of dimeric sodium proton antiporter NhaA, at pH 6.0, crystallized with chimeric… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8ZRZ3 · AlphaFold monomer V2.0 prediction for NA(+)/H(+) antiporter nhaa (Q8ZRZ3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8ZRZ3
- Elsewhere: RCSB PDB 7A0X · PDBe 7A0X · UniProt Q8ZRZ3
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