Research workbench
Complement component C2A, the catalytic fragment of C3- and C5- convertase of human complement
Analyse Complement component C2A, the catalytic fragment of C3- and C5- convertase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ODP
- Type
- protein
- Length
- 490 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C2
- EC
- 3.4.21.43
- UniProt
- P06681
- Ligands
- NAG, MG
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C2 (EC 3.4.21.43) | protein | 490 | 29% helix, 25% strand | P06681 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.51 | 0.78 | 24 | empty |
| 2 | 92 | 0.49 | 0.82 | 20 | NAG |
| 3 | 86 | 0.45 | 0.81 | 21 | empty |
| 4 | 107 | 0.42 | 0.77 | 23 | empty |
| 5 | 120 | 0.41 | 0.76 | 22 | empty |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2ODP · Complement component C2a, the catalytic fragment of C3- and C5-convertase of human… · the same entry in another collection · chain A against A, TM-score 1.00
- P06681 · AlphaFold monomer V2.0 prediction for complement C2 (P06681) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P06681
- Elsewhere: RCSB PDB 2ODP · PDBe 2ODP · UniProt P06681
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