Research workbench
Crystal structure of 12CA5 fv-clasp fragment with its antigen peptide
Analyse Crystal structure of 12CA5 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
- 5XCU
- Type
- protein
- Length
- 674 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera; Vl-SARAH(S37C) CHIMERA,VL-SARAH(S37C)…
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera | protein | 171 | 28% helix, 33% strand | — |
| B | Vl-SARAH(S37C) CHIMERA,VL-SARAH(S37C) chimera | protein | 165 | 27% helix, 33% strand | — |
| C, F | Ha peptide | protein | 8 | 0% helix, 0% strand | — |
| D | VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera | protein | 165 | 28% helix, 34% strand | — |
| E | Vl-SARAH(S37C) CHIMERA,VL-SARAH(S37C) chimera | protein | 157 | 25% helix, 35% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.78 | 0.80 | 111 | empty |
| 2 | 629 | 0.69 | 0.77 | 58 | empty |
| 3 | 167 | 0.57 | 0.82 | 30 | SO4 |
| 4 | 89 | 0.36 | 0.75 | 17 | empty |
| 5 | 91 | 0.36 | 0.75 | 20 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2644 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2379 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 465 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 246 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5XCU · Crystal structure of 12CA5 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 5XCU · PDBe 5XCU
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