Research workbench
Ternary complex of human complement C5 with ornithodoros moubata omci and rhipicephalus microplus RACI2
Analyse Ternary complex of human complement C5 with ornithodoros moubata omci and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HCD
- Type
- protein
- Length
- 1,825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Complement inhibitor; Rhipicephalus microplus RACI2
- UniProt
- P01031, Q5YD59
- Ligands
- CYS, NAG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Complement C5 | protein | 647 | 5% helix, 50% strand | P01031 |
| A | Complement C5 | protein | 981 | 28% helix, 30% strand | P01031 |
| C | Complement inhibitor | protein | 148 | 17% helix, 46% strand | Q5YD59 |
| D | Rhipicephalus microplus RACI2 | protein | 49 | 0% helix, 41% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.79 | 0.82 | 92 | CYS |
| 2 | 650 | 0.76 | 0.82 | 58 | empty |
| 3 | 460 | 0.75 | 0.84 | 55 | empty |
| 4 | 806 | 0.75 | 0.79 | 88 | empty |
| 5 | 223 | 0.73 | 0.88 | 33 | empty |
Interfaces
4 interfaces between chains.
- B–A · 4437 Ų buried · 68 hydrogen bonds · protein-protein
- A–C · 1137 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 565 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 503 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 5HCD · Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Rhipicephalus… · 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
- Elsewhere: RCSB PDB 5HCD · PDBe 5HCD · UniProt P01031 · UniProt Q5YD59
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