MolNFT v1 · #81161 · protein
Crystal structure of adenosine 5'-phosphosulfate kinase from arabidopsis thaliana in complex with amppnp and aps
3UIE · Adenylyl-sulfate kinase 1, chloroplastic: “Crystal structure of adenosine 5'-phosphosulfate kinase from arabidopsis thaliana in complex with amppnp and…”. X-ray diffraction, 3 ligands (ADX, ANP, MG), 7 pockets (best druggability…
- PDB
- 3UIE
- Type
- protein
- Length
- 575 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylyl-sulfate kinase 1, chloroplastic
- EC
- 2.7.1.25
- UniProt
- Q43295
- Ligands
- ADX, ANP, MG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylyl-sulfate kinase 1, chloroplastic (EC 2.7.1.25) | protein | 191 | 43% helix, 14% strand | Q43295 |
| B | Adenylyl-sulfate kinase 1, chloroplastic (EC 2.7.1.25) | protein | 197 | 42% helix, 14% strand | Q43295 |
| C | Adenylyl-sulfate kinase 1, chloroplastic (EC 2.7.1.25) | protein | 187 | 44% helix, 14% strand | Q43295 |
Ligands and binding sites
- ADX · Adenosine-5'-phosphosulfate · ligand · 3 copies · chains A, B, C
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.69 | 0.85 | 38 | ADX, ANP, MG |
| 2 | 230 | 0.60 | 0.80 | 33 | ADX, ANP, MG |
| 3 | 194 | 0.58 | 0.81 | 32 | ADX, ANP, MG |
| 4 | 191 | 0.58 | 0.81 | 29 | empty |
| 5 | 206 | 0.44 | 0.73 | 29 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1951 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 177 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3UIE · Crystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis Thaliana in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q43295 · AlphaFold monomer V2.0 prediction for adenylyl-sulfate kinase 1, chloroplastic (Q43295) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q43295
- Elsewhere: RCSB PDB 3UIE · PDBe 3UIE · UniProt Q43295
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