MolNFT v1 · #117501 · protein
Structure of the antibody 7968 with human complement factor H-derived peptide
5EA0 · Heavy chain of antibody 7968 Fab fragment: “Structure of the antibody 7968 with human complement factor H-derived peptide”. X-ray diffraction, 1 ligand (NH2), 4 pockets (best druggability 0.69). MolNFT v1 #117501 on GenesisL1: 3D…
- PDB
- 5EA0
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of antibody 7968 Fab fragment; Light chain of antibody 7968 Fab fragment…
- UniProt
- P36980
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of antibody 7968 Fab fragment | protein | 214 | 7% helix, 53% strand | — |
| L | Light chain of antibody 7968 Fab fragment | protein | 219 | 6% helix, 52% strand | — |
| P | Complement factor H-related protein 2 | protein | 11 | 27% helix, 0% strand | P36980 |
Ligands and binding sites
- NH2 · Amino group · ion · chains H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.69 | 0.75 | 69 | empty |
| 2 | 196 | 0.48 | 0.75 | 31 | empty |
| 3 | 108 | 0.38 | 0.74 | 21 | empty |
| 4 | 70 | 0.29 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1725 Ų buried · 11 hydrogen bonds · protein-protein
- H–P · 439 Ų buried · 12 hydrogen bonds · protein-protein
- L–P · 266 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EA0 · Structure of the antibody 7968 with human complement factor H-derived peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P36980 · AlphaFold monomer V2.0 prediction for complement factor H-related protein 2 (P36980) · a predicted model of the same protein · chain P against A, TM-score 0.28
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 P36980
- Elsewhere: RCSB PDB 5EA0 · PDBe 5EA0 · UniProt P36980
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