MolNFT v1 · #69444 · protein
The structure of serum amyloid P component bound to phosphoethanolamine
3KQR · Serum amyloid P-component: “The structure of serum amyloid P component bound to phosphoethanolamine”. X-ray diffraction, 3 ligands (OPE, NAG, CA), 8 pockets (best druggability 0.53). MolNFT v1 #69444 on GenesisL1: 3D structure…
- PDB
- 3KQR
- 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
- OPE, NAG, CA
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Serum amyloid P-component | protein | 204 | 6% helix, 46% strand | P02743 |
Ligands and binding sites
- OPE · Phosphoric acid mono-(2-amino-ethyl) ester · 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
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 | 112 | 0.53 | 0.82 | 36 | empty |
| 2 | 82 | 0.32 | 0.74 | 16 | empty |
| 3 | 85 | 0.31 | 0.73 | 15 | empty |
| 4 | 80 | 0.31 | 0.73 | 14 | empty |
| 5 | 79 | 0.31 | 0.73 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 773 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 760 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 758 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 751 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 748 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3KQR · The structure of serum amyloid p component bound to phosphoethanolamine · 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 3KQR · PDBe 3KQR · UniProt P02743
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