MolNFT v1 · #172383 · protein
Structure of dimeric sodium proton antiporter nhaa, at pH 8.5, crystallized with chimeric Fab antibodies
7A0W · NA(+)/H(+) antiporter nhaa: “Structure of dimeric sodium proton antiporter nhaa, at pH 8.5, crystallized with chimeric Fab antibodies”. X-ray diffraction, 4 ligands (3PH, CDL, CL), 17 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 7A0W
- Type
- protein
- Length
- 1,593 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, CL, PO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA(+)/H(+) antiporter nhaa | protein | 368 | 72% helix, 4% strand | Q8ZRZ3 |
| B | NA(+)/H(+) antiporter nhaa | protein | 373 | 71% helix, 3% strand | Q8ZRZ3 |
| C | Chimeric antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy chain | protein | 213 | 7% helix, 48% strand | — |
| D | Chimeric antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light chain | protein | 207 | 7% helix, 49% strand | — |
| E | Chimeric antibody Fab-F6, heavy CHAIN,CHIMERIC antibody Fab-F6, heavy chain | protein | 223 | 8% helix, 52% strand | — |
| F | Chimeric antibody Fab-F6, light CHAIN,CHIMERIC antibody Fab-F6, light chain | protein | 209 | 5% helix, 51% strand | — |
Ligands and binding sites
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 4 copies · chains A, B
- CDL · Cardiolipin · ligand · chains A, B
- CL · Chloride ion · ion · 3 copies · chains C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.78 | 0.80 | 85 | PG4 |
| 2 | 1017 | 0.78 | 0.80 | 87 | PG4 |
| 3 | 1098 | 0.70 | 0.73 | 80 | CDL, 3PH |
| 4 | 427 | 0.61 | 0.76 | 47 | empty |
| 5 | 210 | 0.60 | 0.81 | 30 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1999 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1776 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 663 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 613 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 603 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7A0W · Structure of dimeric sodium proton antiporter NhaA, at pH 8.5, 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 7A0W · PDBe 7A0W · UniProt Q8ZRZ3
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