MolNFT v1 · #146584 · protein
Complement component POLYC9
6DLW · Complement component C9: “Complement component POLYC9”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #146584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DLW
- Type
- protein
- Length
- 10,120 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement component C9
- UniProt
- P02748
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V | Complement component C9 | protein | 460 | 13% helix, 35% strand | P02748 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
- BMA · beta-D-mannopyranose · sugar · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
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 | 1092 | 0.87 | 0.88 | 148 | empty |
| 2 | 978 | 0.83 | 0.84 | 98 | empty |
| 3 | 990 | 0.83 | 0.84 | 105 | empty |
| 4 | 1022 | 0.82 | 0.84 | 101 | empty |
| 5 | 747 | 0.82 | 0.85 | 92 | empty |
Interfaces
22 interfaces between chains.
- H–I · 4078 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 4077 Ų buried · 65 hydrogen bonds · protein-protein
- U–V · 4076 Ų buried · 66 hydrogen bonds · protein-protein
- M–N · 4075 Ų buried · 65 hydrogen bonds · protein-protein
- D–E · 4073 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 220 disulfide, 44 glycan (disulfide, C-mannosylation, O-glycosylation).
Compared structures
- 6DLW · Complement component polyC9 · the same entry in another collection · chain K against K, TM-score 1.00
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 P02748
- Elsewhere: RCSB PDB 6DLW · PDBe 6DLW · UniProt P02748
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