Research workbench
Structure of the sodium proton antiporter MJNHAP1 from methanocaldococcus jannaschii at pH 8.
Analyse Structure of the sodium proton antiporter MJNHAP1 from methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CZB
- Type
- protein
- Length
- 1,655 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA(+)/H(+) antiporter 1
- UniProt
- Q60362
- Ligands
- TAM, K
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA(+)/H(+) antiporter 1 | protein | 415 | 77% helix, 0% strand | Q60362 |
| B | NA(+)/H(+) antiporter 1 | protein | 419 | 79% helix, 0% strand | Q60362 |
| C | NA(+)/H(+) antiporter 1 | protein | 404 | 76% helix, 0% strand | Q60362 |
| D | NA(+)/H(+) antiporter 1 | protein | 417 | 78% helix, 0% strand | Q60362 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- K · Potassium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.86 | 0.90 | 43 | empty |
| 2 | 1088 | 0.86 | 0.86 | 113 | empty |
| 3 | 613 | 0.85 | 0.89 | 48 | empty |
| 4 | 1172 | 0.84 | 0.85 | 129 | empty |
| 5 | 455 | 0.77 | 0.85 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2292 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 2206 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 755 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 697 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 643 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4CZB · Structure of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii at… · the same entry in another collection · chain D against D, TM-score 1.00
- Q60362 · AlphaFold monomer V2.0 prediction for NA(+)/H(+) antiporter 1 (Q60362) · 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 Q60362
- Elsewhere: RCSB PDB 4CZB · PDBe 4CZB · UniProt Q60362
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