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
- 4AVV
- 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
- GHE, NAG, SIA, MAN, GAL, BMA, CD
- Pockets
- 12 · best druggability 0.48
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
- 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, D, A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains E, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- CD · Cadmium ion · metal · 35 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 8 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.48 | 0.82 | 17 | empty |
| 2 | 81 | 0.48 | 0.82 | 16 | empty |
| 3 | 83 | 0.47 | 0.81 | 17 | empty |
| 4 | 79 | 0.47 | 0.82 | 15 | empty |
| 5 | 66 | 0.45 | 0.82 | 28 | empty |
Interfaces
5 interfaces between chains.
- D–E · 749 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 748 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 747 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 741 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, 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 4AVV · PDBe 4AVV · UniProt P02743
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