Research workbench
Ternary complex of human complement C5 with ornithodoros moubata omci and dermacentor andersoni RACI3.
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
- 5HCC
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Complement inhibitor; Dermacentor andersoni RACI3
- UniProt
- P01031, Q5YD59
- Ligands
- CYS, NAG
- Pockets
- 20 · best druggability 0.77
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 | 982 | 27% helix, 30% strand | P01031 |
| C | Complement inhibitor | protein | 148 | 17% helix, 46% strand | Q5YD59 |
| D | Dermacentor andersoni RACI3 | protein | 47 | 0% helix, 49% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, A, C, D
- DIO · 1,4-diethylene dioxide · additive · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.77 | 0.86 | 62 | CYS |
| 2 | 576 | 0.76 | 0.83 | 66 | EDO |
| 3 | 462 | 0.75 | 0.84 | 55 | empty |
| 4 | 236 | 0.73 | 0.87 | 35 | empty |
| 5 | 97 | 0.73 | 0.94 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–A · 4417 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 476 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 5HCC · Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Dermacentor… · 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 5HCC · PDBe 5HCC · UniProt P01031 · UniProt Q5YD59
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