MolNFT v1 · #120819 · protein
Ternary complex of human complement C5 with ornithodoros moubata omci and rhipicephalus microplus RACI2
5HCD: “Ternary complex of human complement C5 with ornithodoros moubata omci and rhipicephalus microplus RACI2”. X-ray diffraction, 2 ligands (CYS, NAG), 20 pockets (best druggability 0.79). MolNFT v1 #120819 on GenesisL1: 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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