Research workbench
Ternary host recognition complex of complement factor H, C3D, and sialic acid
Analyse Ternary host recognition complex of complement factor H, C3D, and sialic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ONT
- Type
- protein
- Length
- 1,255 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor H; Complement C3D fragment
- UniProt
- P08603, P01024
- Ligands
- BGC, GAL, SIA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Complement factor H | protein | 124 | 6% helix, 39% strand | P08603 |
| A | Complement C3D fragment | protein | 295 | 63% helix, 2% strand | P01024 |
| D, E | Complement factor H | protein | 126 | 6% helix, 38% strand | P08603 |
| B | Complement C3D fragment | protein | 292 | 62% helix, 2% strand | P01024 |
| C | Complement C3D fragment | protein | 292 | 62% helix, 2% strand | P01024 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains F, D, B, E
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains F, D, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains F, D, E
- GOL · Glycerol · additive · 7 copies · chains A, D, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.83 | 0.85 | 97 | SIA, GOL |
| 2 | 694 | 0.74 | 0.80 | 68 | empty |
| 3 | 104 | 0.60 | 0.87 | 19 | GOL |
| 4 | 152 | 0.52 | 0.79 | 22 | empty |
| 5 | 103 | 0.48 | 0.80 | 16 | GOL |
Interfaces
7 interfaces between chains.
- A–D · 938 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 847 Ų buried · 15 hydrogen bonds · protein-protein
- F–B · 839 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 760 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 601 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 4ONT · Ternary host recognition complex of complement factor H, C3d, and sialic acid · the same entry in another collection · chain C against C, TM-score 1.00
- P08603 · AlphaFold monomer V2.0 prediction for complement factor H (P08603) · a predicted model of the same protein · chain E against A, TM-score 0.92
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P08603
- Every structure of UniProt P01024
- Elsewhere: RCSB PDB 4ONT · PDBe 4ONT · UniProt P08603 · UniProt P01024
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