Research workbench
Human octameric paics in complex with saicar, AMP-pnp, and magnesium
Analyse Human octameric paics in complex with saicar, AMP-pnp, and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YB9
- Type
- protein
- Length
- 838 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional protein ADE2
- EC
- 6.3.2.6, 4.1.1.21
- UniProt
- P22234
- Ligands
- ANP, OK8, MG
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Multifunctional protein ADE2 (EC 6.3.2.6, 4.1.1.21) | protein | 419 | 41% helix, 25% strand | P22234 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- OK8 · (2~{S})-2-[[5-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]imidazol-4-yl]car bonylamino]butanedioic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, 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 | 734 | 0.74 | 0.79 | 57 | ANP, OK8, MG |
| 2 | 754 | 0.73 | 0.78 | 57 | ANP, OK8, MG |
| 3 | 576 | 0.70 | 0.79 | 71 | EDO |
| 4 | 285 | 0.58 | 0.78 | 54 | empty |
| 5 | 80 | 0.53 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1971 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6YB9 · Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium · the same entry in another collection · chain A against A, TM-score 1.00
- P22234 · AlphaFold monomer V2.0 prediction for multifunctional protein ADE2 (P22234) · 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 P22234
- Elsewhere: RCSB PDB 6YB9 · PDBe 6YB9 · UniProt P22234
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