Research workbench
Structure of tick complement inhibitor CIRPT1 complexed with macroglobubulin domain 4 of human complement C5
Analyse Structure of tick complement inhibitor CIRPT1 complexed with macroglobubulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RPT
- Type
- protein
- Length
- 595 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Putative 8.9 kda family member
- UniProt
- P01031, L7MB58
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, C | Complement C5 | protein | 112 | 3% helix, 50% strand | P01031 |
| F, B, D | Putative 8.9 kda family member | protein | 86 | 0% helix, 44% strand | L7MB58 |
| A | Complement C5 | protein | 113 | 0% helix, 50% strand | P01031 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains E, F, A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.80 | 0.81 | 137 | GOL |
| 2 | 180 | 0.59 | 0.82 | 35 | GOL |
| 3 | 149 | 0.50 | 0.79 | 26 | empty |
| 4 | 134 | 0.49 | 0.79 | 24 | empty |
| 5 | 103 | 0.39 | 0.76 | 28 | empty |
Interfaces
10 interfaces between chains.
- E–F · 826 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 818 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 10 hydrogen bonds · protein-protein
- E–C · 353 Ų buried · 2 hydrogen bonds · protein-protein
- F–A · 294 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6RPT · Structure of tick complement inhibitor CirpT1 complexed with macroglobubulin domain 4 of… · the same entry in another collection · chain D against D, TM-score 1.00
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P01031
- Every structure of UniProt L7MB58
- Elsewhere: RCSB PDB 6RPT · PDBe 6RPT · UniProt P01031 · UniProt L7MB58
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