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
- 5XCR
- Type
- protein
- Length
- 662 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vh-SARAH(Y35C) chimera; Vl-SARAH(M24C) chimera; C8 peptide
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vh-SARAH(Y35C) chimera | protein | 166 | 31% helix, 34% strand | — |
| B | Vl-SARAH(M24C) chimera | protein | 160 | 30% helix, 37% strand | — |
| C | C8 peptide | protein | 7 | 0% helix, 0% strand | — |
| D | Vh-SARAH(Y35C) chimera | protein | 161 | 33% helix, 35% strand | — |
| E | Vl-SARAH(M24C) chimera | protein | 162 | 30% helix, 37% strand | — |
| F | C8 peptide | protein | 6 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.78 | 0.80 | 78 | empty |
| 2 | 938 | 0.78 | 0.80 | 97 | empty |
| 3 | 251 | 0.53 | 0.76 | 29 | empty |
| 4 | 91 | 0.47 | 0.80 | 17 | empty |
| 5 | 91 | 0.37 | 0.76 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2606 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2382 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 323 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 317 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5XCR · 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 5XCR · PDBe 5XCR
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