MolNFT v1 · #86082 · protein
Structure of N-acetyl-L-proline bound to serum amyloid P component
4AVS · Serum amyloid P-component: “Structure of N-acetyl-L-proline bound to serum amyloid P component”. X-ray diffraction, 3 ligands (N7P, NAG, CA), 8 pockets (best druggability 0.59). MolNFT v1 #86082 on GenesisL1: 3D structure, binding…
- PDB
- 4AVS
- 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
- N7P, NAG, CA
- Pockets
- 8 · best druggability 0.59
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
- N7P · 1-acetyl-L-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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.59 | 0.91 | 23 | empty |
| 2 | 57 | 0.57 | 0.90 | 24 | empty |
| 3 | 73 | 0.54 | 0.86 | 22 | empty |
| 4 | 104 | 0.35 | 0.74 | 16 | empty |
| 5 | 81 | 0.32 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 766 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 762 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 761 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 753 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 747 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4AVS · Structure of N-Acetyl-L-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 4AVS · PDBe 4AVS · UniProt P02743
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