Research workbench
Adenosine-5'-phosphosulfate reductase im complex with products
Analyse Adenosine-5'-phosphosulfate reductase im complex with products in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FJB
- Type
- protein
- Length
- 1,582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylylsulfate reductase, subunit a; Adenylylsulfate reductase, subunit B
- EC
- 1.8.99.2
- Ligands
- SF4, AMP, SFD, NA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenylylsulfate reductase, subunit a (EC 1.8.99.2) | protein | 642 | 40% helix, 17% strand | — |
| B, D | Adenylylsulfate reductase, subunit B (EC 1.8.99.2) | protein | 149 | 13% helix, 23% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, C
- SFD · (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl)methoxy)(hydroxy)phosphoryloxy)(hydroxy)phosphoryloxy)-2,3,4-trihydroxypentyl)-7,8-dimethyl-2,4-dioxo-2,3,4,4A-tetrahydrobenzo[g]pteridine-5(10H)-sulfonic acid · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.86 | 0.89 | 88 | SFD, AMP |
| 2 | 709 | 0.85 | 0.89 | 87 | NA, SFD, AMP |
| 3 | 678 | 0.83 | 0.87 | 82 | empty |
| 4 | 222 | 0.83 | 0.96 | 50 | empty |
| 5 | 103 | 0.63 | 0.88 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4509 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 4478 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 1707 Ų buried · 32 hydrogen bonds · protein-protein
- C–B · 868 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 850 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2FJB · Adenosine-5'-phosphosulfate reductase im complex with products · 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
- Elsewhere: RCSB PDB 2FJB · PDBe 2FJB
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