MolNFT v1 · #128854 · protein
The structure of complement complex
5O32 · Complement C3: “The structure of complement complex”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 20 pockets (best druggability 0.86). MolNFT v1 #128854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O32
- Type
- protein
- Length
- 4,912 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Complement factor H,COMPLEMENT factor H; Complement factor I
- EC
- 3.4.21.45
- UniProt
- P01024, P08603, P05156
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Complement C3 | protein | 640 | 7% helix, 52% strand | P01024 |
| B, F | Complement C3 | protein | 903 | 25% helix, 32% strand | P01024 |
| C, G | Complement factor H,COMPLEMENT factor H | protein | 371 | 2% helix, 35% strand | P08603 |
| D, H | Complement factor I (EC 3.4.21.45) | protein | 301 | 13% helix, 18% strand | P05156 |
| I, J | Complement factor I (EC 3.4.21.45) | protein | 241 | 9% helix, 30% strand | P05156 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, E, F, D, I, H, J
- BMA · beta-D-mannopyranose · sugar · 6 copies
- CA · Calcium ion · metal · 6 copies · chains A, D, E, H
- MLI · Malonate ion · additive · chains I, J
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 | 940 | 0.86 | 0.88 | 108 | empty |
| 2 | 435 | 0.81 | 0.89 | 49 | empty |
| 3 | 1030 | 0.80 | 0.81 | 127 | empty |
| 4 | 1005 | 0.79 | 0.81 | 88 | empty |
| 5 | 900 | 0.77 | 0.80 | 92 | empty |
Interfaces
25 interfaces between chains.
- A–B · 5166 Ų buried · 72 hydrogen bonds · protein-protein
- E–F · 5112 Ų buried · 64 hydrogen bonds · protein-protein
- F–G · 2281 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2204 Ų buried · 24 hydrogen bonds · protein-protein
- F–J · 1269 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
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 P01024
- Every structure of UniProt P08603
- Every structure of UniProt P05156
- Elsewhere: RCSB PDB 5O32 · PDBe 5O32 · UniProt P01024 · UniProt P08603 · UniProt P05156
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.