Research workbench
Factor H enhancing human antibody fragment (Fab) to meningococcal factor H binding protein
Analyse Factor H enhancing human antibody fragment (Fab) to meningococcal factor H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KE1
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma, kappa light chain; Immunoglobulin gamma, heavy chain fd fragment
- Ligands
- LI, NA, SO4, CL
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Immunoglobulin gamma, kappa light chain | protein | 214 | 8% helix, 53% strand | — |
| A | Immunoglobulin gamma, heavy chain fd fragment | protein | 217 | 10% helix, 51% strand | — |
| C | Immunoglobulin gamma, heavy chain fd fragment | protein | 216 | 8% helix, 51% strand | — |
Ligands and binding sites
- LI · Lithium ion · metal · 2 copies · chains A, C
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 7 copies · chains B, A, D, C
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.71 | 0.75 | 124 | SO4 |
| 2 | 692 | 0.70 | 0.78 | 79 | SO4 |
| 3 | 90 | 0.36 | 0.75 | 17 | empty |
| 4 | 83 | 0.35 | 0.76 | 20 | empty |
| 5 | 50 | 0.27 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–A · 1647 Ų buried · 14 hydrogen bonds · protein-protein
- D–C · 1638 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 664 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7KE1 · Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7KE1 · PDBe 7KE1
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