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Structure of the sodium proton antiporter panhap from pyrococcus abyssii with bound thallium ion.
Analyse Structure of the sodium proton antiporter panhap from pyrococcus abyssii with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CZA
- Type
- protein
- Length
- 839 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA+/H+ antiporter, putative
- UniProt
- Q9UZ55
- Ligands
- TAM, TL
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA+/H+ antiporter, putative | protein | 420 | 81% helix, 0% strand | Q9UZ55 |
| B | NA+/H+ antiporter, putative | protein | 419 | 80% helix, 0% strand | Q9UZ55 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 4 copies · chains A, B
- TL · Thallium (I) ion · metal · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · chains A, B
- UND · Undecane · additive · chains B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.85 | 0.85 | 73 | empty |
| 2 | 558 | 0.71 | 0.79 | 47 | TAM |
| 3 | 505 | 0.70 | 0.79 | 33 | ACT |
| 4 | 239 | 0.58 | 0.78 | 24 | empty |
| 5 | 192 | 0.57 | 0.80 | 32 | TAM |
Interfaces
1 interface between chains.
- A–B · 1842 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4CZA · Structure of the sodium proton antiporter PaNhaP from Pyrococcus abyssii with bound… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9UZ55
- Elsewhere: RCSB PDB 4CZA · PDBe 4CZA · UniProt Q9UZ55
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