Research workbench
Serum amyloid P component co-crystallised with mobdg at neutral pH
Analyse Serum amyloid P component co-crystallised with mobdg at neutral pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GYK
- 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
- CDG, CA
- Pockets
- 7 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Serum amyloid P-component | protein | 204 | 5% helix, 45% strand | P02743 |
Ligands and binding sites
- CDG · Methyl 4,6-O-[(1R)-1-carboxyethylidene]-beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.46 | 0.82 | 31 | empty |
| 2 | 98 | 0.33 | 0.73 | 16 | empty |
| 3 | 76 | 0.29 | 0.73 | 15 | empty |
| 4 | 75 | 0.29 | 0.72 | 16 | empty |
| 5 | 78 | 0.29 | 0.72 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 802 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 790 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 784 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 781 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1GYK · Serum Amyloid P Component co-crystallised with MOBDG at neutral pH · 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 1GYK · PDBe 1GYK · UniProt P02743
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