Research workbench
Crystal structure of the mouse C5A-desarg anaphylatoxin
Analyse Crystal structure of the mouse C5A-desarg anaphylatoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P3B
- Type
- protein
- Length
- 276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5
- UniProt
- P06684
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C5 | protein | 69 | 67% helix, 0% strand | P06684 |
| B | Complement C5 | protein | 69 | 68% helix, 0% strand | P06684 |
| C | Complement C5 | protein | 70 | 67% helix, 0% strand | P06684 |
| D | Complement C5 | protein | 68 | 69% helix, 0% strand | P06684 |
Ligands and binding sites
- FMT · Formic acid · additive · 15 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.81 | 0.98 | 21 | FMT |
| 2 | 313 | 0.52 | 0.74 | 35 | empty |
| 3 | 130 | 0.40 | 0.75 | 15 | empty |
| 4 | 53 | 0.28 | 0.74 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 674 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 326 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 P06684
- Elsewhere: RCSB PDB 4P3B · PDBe 4P3B · UniProt P06684
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