Research workbench
Structure of human complement C4 rebuilt using imdff
Analyse Structure of human complement C4 rebuilt using imdff in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JPN
- Type
- protein
- Length
- 1,638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C4-a
- UniProt
- P0C0L4
- Ligands
- NAG, MAN, BMA, A2G, PBM
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C4-a | protein | 651 | 7% helix, 50% strand | P0C0L4 |
| B | Complement C4-a | protein | 697 | 34% helix, 25% strand | P0C0L4 |
| C | Complement C4-a | protein | 290 | 15% helix, 36% strand | P0C0L4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains B
- PBM · Trimethyl lead ion · metal · 4 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.76 | 0.96 | 28 | empty |
| 2 | 194 | 0.73 | 0.89 | 37 | empty |
| 3 | 624 | 0.72 | 0.80 | 52 | empty |
| 4 | 361 | 0.69 | 0.82 | 34 | empty |
| 5 | 330 | 0.68 | 0.82 | 47 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4432 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 4309 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 5 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- P0C0L4 · AlphaFold monomer V2.0 prediction for complement C4-a (P0C0L4) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P0C0L4
- Elsewhere: RCSB PDB 5JPN · PDBe 5JPN · UniProt P0C0L4
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