MolNFT v1 · #163024 · protein
Structure of human complement C5 complexed with tick inhibitors omci, RACI1 and CIRPT1
6RQJ: “Structure of human complement C5 complexed with tick inhibitors omci, RACI1 and CIRPT1”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.78). MolNFT v1 #163024 on GenesisL1: 3D structure, binding sites and…
- 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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