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The structure of C-reactive protein bound to phosphoethanolamine
Analyse The structure of C-reactive protein bound to phosphoethanolamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L2Y
- Type
- protein
- Length
- 4,120 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-reactive protein
- UniProt
- P02741
- Ligands
- OPE, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | C-reactive protein | protein | 206 | 9% helix, 44% strand | P02741 |
Ligands and binding sites
- OPE · Phosphoric acid mono-(2-amino-ethyl) ester · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- CA · Calcium ion · metal · 40 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.83 | 0.85 | 121 | empty |
| 2 | 1155 | 0.83 | 0.84 | 160 | empty |
| 3 | 1011 | 0.82 | 0.83 | 106 | empty |
| 4 | 480 | 0.80 | 0.87 | 44 | empty |
| 5 | 398 | 0.71 | 0.82 | 56 | empty |
Interfaces
35 interfaces between chains.
- L–M · 709 Ų buried · 12 hydrogen bonds · protein-protein
- R–S · 706 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 702 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 701 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 697 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3L2Y · The structure of C-reactive protein bound to phosphoethanolamine · the same entry in another collection · chain J against J, 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 P02741
- Elsewhere: RCSB PDB 3L2Y · PDBe 3L2Y · UniProt P02741
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