Research workbench
Crystal structure of native heptameric sap-like pentraxin from limulus polyphemus
Analyse Crystal structure of native heptameric sap-like pentraxin from limulus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FLP
- Type
- protein
- Length
- 3,038 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sap-like pentraxin
- UniProt
- Q8WQK3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Sap-like pentraxin | protein | 217 | 6% helix, 49% strand | Q8WQK3 |
Ligands and binding sites
- CA · Calcium ion · metal · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.81 | 0.83 | 87 | empty |
| 2 | 930 | 0.81 | 0.83 | 98 | empty |
| 3 | 865 | 0.81 | 0.83 | 90 | empty |
| 4 | 887 | 0.80 | 0.82 | 98 | empty |
| 5 | 900 | 0.80 | 0.82 | 98 | empty |
Interfaces
28 interfaces between chains.
- G–H · 892 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 890 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 889 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 880 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 877 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 3FLP · Crystal structure of native heptameric SAP-like pentraxin from Limulus polyphemus · the same entry in another collection · 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 Q8WQK3
- Elsewhere: RCSB PDB 3FLP · PDBe 3FLP · UniProt Q8WQK3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.