Research workbench
Structure of cphpc bound to serum amyloid P component
Analyse Structure of cphpc 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
- 4AVT
- Type
- protein
- Length
- 2,040 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum amyloid P-component
- UniProt
- P02743
- Ligands
- GHE, NAG, CA
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Serum amyloid P-component | protein | 204 | 5% helix, 47% strand | P02743 |
Ligands and binding sites
- GHE · (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CA · Calcium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.59 | 0.75 | 44 | GHE, CA |
| 2 | 451 | 0.59 | 0.75 | 32 | GHE |
| 3 | 404 | 0.58 | 0.75 | 30 | GHE |
| 4 | 389 | 0.55 | 0.74 | 30 | GHE |
| 5 | 340 | 0.52 | 0.73 | 31 | GHE |
Interfaces
15 interfaces between chains.
- C–E · 782 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 779 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 776 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 775 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan (N-glycosylation).
Compared structures
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 4AVT · PDBe 4AVT · UniProt P02743
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