Research workbench
Crystal structure of assimilatory adenosine 5'- phosphosulfate reductase with bound aps
Analyse Crystal structure of assimilatory adenosine 5'- phosphosulfate reductase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GOY
- Type
- protein
- Length
- 1,780 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine phosphosulfate reductase
- EC
- 1.8.4.10
- UniProt
- O05927
- Ligands
- SF4, ADX
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Adenosine phosphosulfate reductase (EC 1.8.4.10) | protein | 222 | 46% helix, 10% strand | O05927 |
| B, D, F, H | Adenosine phosphosulfate reductase (EC 1.8.4.10) | protein | 223 | 43% helix, 10% strand | O05927 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ADX · Adenosine-5'-phosphosulfate · ligand · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.75 | 0.83 | 47 | SF4, ADX |
| 2 | 491 | 0.75 | 0.83 | 49 | SF4, ADX |
| 3 | 491 | 0.74 | 0.83 | 51 | SF4, ADX |
| 4 | 479 | 0.74 | 0.83 | 50 | SF4, ADX |
| 5 | 527 | 0.74 | 0.82 | 53 | SF4 |
Interfaces
9 interfaces between chains.
- F–H · 1359 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1358 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 1261 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1260 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 745 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2GOY · Crystal structure of assimilatory adenosine 5'-phosphosulfate reductase with bound APS · the same entry in another collection · chain H against H, TM-score 1.00
- O05927 · AlphaFold monomer V2.0 prediction for adenosine 5'-phosphosulfate reductase (O05927) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O05927
- Elsewhere: RCSB PDB 2GOY · PDBe 2GOY · UniProt O05927
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