Research workbench
Crystal structure of the N-domain of HMA6, a copper-transporting P- type ATPase
Analyse Crystal structure of the N-domain of HMA6, a copper-transporting P- type ATPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LBD
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-transporting ATPase PAA1, chloroplastic
- EC
- 3.6.3.54
- UniProt
- Q9SZC9
- Ligands
- IOD, NH4, CL
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-transporting ATPase PAA1, chloroplastic (EC 3.6.3.54) | protein | 115 | 30% helix, 30% strand | Q9SZC9 |
| B | Copper-transporting ATPase PAA1, chloroplastic (EC 3.6.3.54) | protein | 108 | 26% helix, 33% strand | Q9SZC9 |
Ligands and binding sites
- IOD · Iodide ion · ion · 5 copies · chains A, B
- NH4 · Ammonium ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.46 | 0.79 | 17 | empty |
| 2 | 94 | 0.40 | 0.77 | 19 | empty |
| 3 | 84 | 0.36 | 0.76 | 24 | CL |
| 4 | 83 | 0.36 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 561 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5LBD · Crystal structure of the N-domain of HMA6, a copper-transporting P-type ATPase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SZC9 · AlphaFold monomer V2.0 prediction for copper-transporting ATPase PAA1, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9SZC9
- Elsewhere: RCSB PDB 5LBD · PDBe 5LBD · UniProt Q9SZC9
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