Research workbench
Pentameric crystal structure of human serum amyloid P-component bound to bis-1,2-{[(Z)-2CARBOXY-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}- ethane.
Analyse Pentameric crystal structure of human serum amyloid P-component bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A3Y
- Type
- protein
- Length
- 1,020 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum amyloid P-component
- UniProt
- P02743
- Ligands
- CPJ, CA
- Pockets
- 6 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Serum amyloid P-component | protein | 204 | 6% helix, 47% strand | P02743 |
Ligands and binding sites
- CPJ · Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane · ligand · 5 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.33 | 0.74 | 15 | empty |
| 2 | 107 | 0.33 | 0.72 | 16 | empty |
| 3 | 86 | 0.32 | 0.73 | 14 | empty |
| 4 | 88 | 0.32 | 0.73 | 16 | empty |
| 5 | 59 | 0.31 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 784 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 782 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 778 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 771 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 770 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2A3Y · Pentameric crystal structure of human serum amyloid P-component bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P02743 · AlphaFold monomer V2.0 prediction for serum amyloid P-component (P02743) · a predicted model of the same protein · 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
- Every structure of UniProt P02743
- Elsewhere: RCSB PDB 2A3Y · PDBe 2A3Y · UniProt P02743
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