Research workbench
IGG1 Fab fragment (of E8 antibody) complexed with horse cytochrome C at 1.8 a resolution
Analyse IGG1 Fab fragment (of E8 antibody) complexed with horse cytochrome C at 1.8 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WEJ
- Type
- protein
- Length
- 541 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E8 antibody; Cytochrome C
- UniProt
- P00004
- Ligands
- ACE, HEM, ZN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | E8 antibody | protein | 214 | 6% helix, 53% strand | — |
| H | E8 antibody | protein | 223 | 9% helix, 49% strand | — |
| F | Cytochrome C | protein | 104 | 41% helix, 2% strand | P00004 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains F
- HEM · Protoporphyrin IX containing Fe · ligand · chains F
- ZN · Zinc ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.76 | 0.91 | 36 | HEM |
| 2 | 507 | 0.62 | 0.75 | 55 | empty |
| 3 | 212 | 0.51 | 0.76 | 40 | empty |
| 4 | 148 | 0.46 | 0.76 | 22 | empty |
| 5 | 76 | 0.32 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2001 Ų buried · 21 hydrogen bonds · protein-protein
- L–F · 376 Ų buried · 10 hydrogen bonds · protein-protein
- H–F · 321 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 cofactor, 1 covalent (disulfide, heme attachment, covalent ligand).
Compared structures
- 1WEJ · IGG1 Fab fragment (of E8 antibody) complexed with horse cytochrome C at 1.8 a resolution · the same entry in another collection · chain L against L, TM-score 1.00
- P00004 · AlphaFold monomer V2.0 prediction for cytochrome C (P00004) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P00004
- Elsewhere: RCSB PDB 1WEJ · PDBe 1WEJ · UniProt P00004
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