Research workbench
Three-dimensional structure of a single chain fv fragment complexed with the peptide GCN4(7P-14P).
Analyse Three-dimensional structure of a single chain fv fragment complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P4B
- Type
- protein
- Length
- 234 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody variable light chain; Antibody variable heavy chain; GCN4(7P-14P) peptide
- UniProt
- P01723, P01820
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody variable light chain | protein | 110 | 8% helix, 53% strand | P01723 |
| H | Antibody variable heavy chain | protein | 112 | 5% helix, 48% strand | P01820 |
| P | GCN4(7P-14P) peptide | protein | 12 | 75% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.27 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 785 Ų buried · 2 hydrogen bonds · protein-protein
- H–P · 421 Ų buried · 7 hydrogen bonds · protein-protein
- L–P · 310 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1P4B · Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide… · the same entry in another collection · chain L against L, TM-score 1.00
- P01723 · AlphaFold monomer V2.0 prediction for ig lambda-1 chain V region (P01723) · a predicted model of the same protein · chain L against A, TM-score 0.83
- P01820 · AlphaFold monomer V2.0 prediction for ig heavy chain V region PJ14 (P01820) · a predicted model of the same protein · chain H against A, TM-score 0.82
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 P01723
- Every structure of UniProt P01820
- Elsewhere: RCSB PDB 1P4B · PDBe 1P4B · UniProt P01723 · UniProt P01820
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