Research workbench
Crystal structure of P20.1 fv-clasp fragment with its antigen peptide
Analyse Crystal structure of P20.1 fv-clasp fragment with its antigen peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XCQ
- Type
- protein
- Length
- 332 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vh-SARAH(Y35C)CHIMERA; Vl-SARAH(M24C) chimera; C8 peptide
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vh-SARAH(Y35C)CHIMERA | protein | 166 | 33% helix, 35% strand | — |
| B | Vl-SARAH(M24C) chimera | protein | 160 | 31% helix, 38% strand | — |
| C | C8 peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.66 | 0.75 | 54 | empty |
| 2 | 150 | 0.41 | 0.74 | 22 | empty |
| 3 | 115 | 0.38 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2498 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 325 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 155 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5XCQ · Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide · the same entry in another collection · chain A against A, 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 5XCQ · PDBe 5XCQ
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