Research workbench
Complement factor H in complex with the GM1 glycan
Analyse Complement factor H in complex with the GM1 glycan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZH1
- Type
- protein
- Length
- 1,228 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Complement factor H
- UniProt
- P01024, P08603
- Ligands
- GAL, SIA, BGC, NGA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 293 | 64% helix, 2% strand | P01024 |
| B | Complement C3 | protein | 292 | 63% helix, 2% strand | P01024 |
| C | Complement C3 | protein | 291 | 64% helix, 2% strand | P01024 |
| D | Complement factor H | protein | 126 | 5% helix, 38% strand | P08603 |
| E | Complement factor H | protein | 122 | 6% helix, 39% strand | P08603 |
| F | Complement factor H | protein | 104 | 7% helix, 30% strand | P08603 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains D, F, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains D, E, F
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains E, F
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains E, F
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.79 | 0.82 | 87 | GOL |
| 2 | 863 | 0.72 | 0.77 | 67 | empty |
| 3 | 320 | 0.64 | 0.80 | 34 | empty |
| 4 | 126 | 0.57 | 0.83 | 18 | GOL |
| 5 | 214 | 0.48 | 0.75 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–D · 939 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 838 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 792 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 769 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 568 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4ZH1 · Complement factor H in complex with the GM1 glycan · the same entry in another collection · chain F against F, 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 0.94
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain C against A, TM-score 0.92
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
- Elsewhere: RCSB PDB 4ZH1 · PDBe 4ZH1 · UniProt P01024 · UniProt P08603
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