Research workbench
Crystal structure of human complement C5 in complex with the K92 bovine knob domain peptide.
Analyse Crystal structure of human complement C5 in complex with the K92 bovine knob… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AD6
- Type
- protein
- Length
- 1,651 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; K92 knob domain
- UniProt
- P01031
- Ligands
- CYS, NAG, BMA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C5 | protein | 971 | 28% helix, 30% strand | P01031 |
| B | Complement C5 | protein | 646 | 6% helix, 49% strand | P01031 |
| C | K92 knob domain | protein | 34 | 12% helix, 21% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.80 | 0.82 | 89 | EDO, CYS |
| 2 | 721 | 0.77 | 0.82 | 68 | empty |
| 3 | 440 | 0.71 | 0.81 | 61 | empty |
| 4 | 136 | 0.70 | 0.90 | 39 | empty |
| 5 | 246 | 0.66 | 0.83 | 34 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 4526 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 707 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 7AD6 · Crystal structure of human complement C5 in complex with the K92 bovine knob domain… · 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
- Elsewhere: RCSB PDB 7AD6 · PDBe 7AD6 · UniProt P01031
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