MolNFT v1 · #139338 · protein
Crystal structure of 12CA5 fv-clasp fragment with its antigen peptide
5XCS · Vh-SARAH(Y35C) chimera: “Crystal structure of 12CA5 fv-clasp fragment with its antigen peptide”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.71). MolNFT v1 #139338 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XCS
- Type
- protein
- Length
- 338 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vh-SARAH(Y35C) chimera; Vl-SARAH(M24C) chimera; Ha peptide
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vh-SARAH(Y35C) chimera | protein | 168 | 28% helix, 33% strand | — |
| B | Vl-SARAH(M24C) chimera | protein | 161 | 27% helix, 35% strand | — |
| C | Ha peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.71 | 0.80 | 62 | SO4 |
| 2 | 55 | 0.35 | 0.78 | 11 | empty |
| 3 | 83 | 0.33 | 0.74 | 18 | empty |
| 4 | 60 | 0.26 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2355 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5XCS · 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 5XCS · PDBe 5XCS
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