Research workbench
Structure of human complement C5 complexed with tick inhibitors omci, RACI1 and CIRPT1
Analyse Structure of human complement C5 complexed with tick inhibitors omci, RACI1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RQJ
- Type
- protein
- Length
- 1,899 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Complement inhibitor; Rhipicephalus appendiculatus RACI1; Putative 8.9 kda…
- UniProt
- P01031, Q5YD59, A0A158RFT5, L7MB58
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C5 | protein | 981 | 27% helix, 26% strand | P01031 |
| C | Complement inhibitor | protein | 147 | 14% helix, 45% strand | Q5YD59 |
| D | Rhipicephalus appendiculatus RACI1 | protein | 46 | 0% helix, 37% strand | A0A158RFT5 |
| B | Complement C5 | protein | 643 | 3% helix, 45% strand | P01031 |
| E | Putative 8.9 kda family member | protein | 82 | 0% helix, 41% strand | L7MB58 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.78 | 0.82 | 71 | empty |
| 2 | 480 | 0.76 | 0.84 | 52 | empty |
| 3 | 546 | 0.75 | 0.82 | 68 | empty |
| 4 | 64 | 0.75 | 0.99 | 15 | empty |
| 5 | 677 | 0.72 | 0.79 | 69 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4668 Ų buried · 54 hydrogen bonds · protein-protein
- B–E · 1212 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1049 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 518 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 342 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6RQJ · Structure of human complement C5 complexed with tick inhibitors OmCI, RaCI1 and CirpT1 · the same entry in another collection · chain A against A, TM-score 1.00
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q5YD59
- Every structure of UniProt A0A158RFT5
- Every structure of UniProt L7MB58
- Elsewhere: RCSB PDB 6RQJ · PDBe 6RQJ · UniProt P01031 · UniProt Q5YD59 · UniProt A0A158RFT5 · UniProt L7MB58
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