Research workbench
Structure of complement C5 in complex with cvf and SSL7
Analyse Structure of complement C5 in complex with cvf and SSL7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PRX
- Type
- protein
- Length
- 6,064 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Cobra venom factor; Superantigen-like protein 7
- UniProt
- P01031, Q91132, D3JIB2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Complement C5 | protein | 1626 | 18% helix, 33% strand | P01031 |
| B, D | Cobra venom factor | protein | 1215 | 8% helix, 49% strand | Q91132 |
| X, Y | Superantigen-like protein 7 | protein | 191 | 16% helix, 39% strand | D3JIB2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.83 | 0.84 | 108 | empty |
| 2 | 381 | 0.82 | 0.91 | 52 | empty |
| 3 | 895 | 0.82 | 0.84 | 96 | empty |
| 4 | 875 | 0.81 | 0.83 | 109 | empty |
| 5 | 1070 | 0.80 | 0.81 | 82 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2569 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2563 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1687 Ų buried · 21 hydrogen bonds · protein-protein
- A–X · 977 Ų buried · 19 hydrogen bonds · protein-protein
- C–Y · 976 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3PRX · Structure of Complement C5 in Complex with CVF and SSL7 · the same entry in another collection · chain Y against Y, TM-score 1.00
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q91132 · AlphaFold monomer V2.0 prediction for cobra venom factor (Q91132) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 Q91132
- Every structure of UniProt D3JIB2
- Elsewhere: RCSB PDB 3PRX · PDBe 3PRX · UniProt P01031 · UniProt Q91132 · UniProt D3JIB2
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