Research workbench
Structure of N-acetyl-D-proline bound to serum amyloid P component
Analyse Structure of N-acetyl-D-proline bound to serum amyloid P component in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AYU
- 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
- N8P, NAG, CA
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Serum amyloid P-component | protein | 204 | 7% helix, 46% strand | P02743 |
Ligands and binding sites
- N8P · N-acetyl-D-proline · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 5 copies · chains C, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.59 | 0.92 | 24 | empty |
| 2 | 94 | 0.49 | 0.82 | 32 | empty |
| 3 | 92 | 0.33 | 0.74 | 15 | empty |
| 4 | 83 | 0.32 | 0.74 | 16 | empty |
| 5 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 775 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 771 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 768 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 767 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 764 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4AYU · Structure of N-Acetyl-D-Proline bound to serum amyloid P component · the same entry in another collection · chain E against E, TM-score 1.00
- P02743 · AlphaFold monomer V2.0 prediction for serum amyloid P-component (P02743) · a predicted model of the same protein · chain D 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 4AYU · PDBe 4AYU · UniProt P02743
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