Research workbench
Structure of a triple mutant of the nhaa dimer, crystallised at low pH
Analyse Structure of a triple mutant of the nhaa dimer, crystallised at low pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ATV
- Type
- protein
- Length
- 1,510 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA(+)/H(+) antiporter nhaa
- UniProt
- P13738
- Ligands
- LMU, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NA(+)/H(+) antiporter nhaa | protein | 381 | 67% helix, 3% strand | P13738 |
| B, D | NA(+)/H(+) antiporter nhaa | protein | 374 | 69% helix, 3% strand | P13738 |
Ligands and binding sites
- LMU · Dodecyl-alpha-D-maltoside · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.74 | 0.77 | 87 | empty |
| 2 | 750 | 0.72 | 0.77 | 60 | SO4 |
| 3 | 898 | 0.71 | 0.76 | 63 | empty |
| 4 | 679 | 0.69 | 0.77 | 55 | SO4, LMU |
| 5 | 52 | 0.68 | 0.97 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 707 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 690 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 429 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 4ATV · Structure of a triple mutant of the nhaa dimer, crystallised at low pH · the same entry in another collection · chain A against A, TM-score 1.00
- P13738 · AlphaFold monomer V2.0 prediction for NA(+)/H(+) antiporter nhaa (P13738) · a predicted model of the same protein · chain B 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 P13738
- Elsewhere: RCSB PDB 4ATV · PDBe 4ATV · UniProt P13738
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