MolNFT v1 · #139339 · protein
Crystal structure of P20.1 fv-clasp fragment with its antigen peptide
5XCT · VH(S112C)-sarah chimera: “Crystal structure of P20.1 fv-clasp fragment with its antigen peptide”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.71). MolNFT v1 #139339 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XCT
- Type
- protein
- Length
- 334 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VH(S112C)-sarah chimera; Vl-SARAH(S37C)CHIMERA; C8 peptide
- Ligands
- CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VH(S112C)-sarah chimera | protein | 167 | 32% helix, 34% strand | — |
| B | Vl-SARAH(S37C)CHIMERA | protein | 161 | 30% helix, 37% strand | — |
| C | C8 peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
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 | 820 | 0.71 | 0.77 | 55 | empty |
| 2 | 147 | 0.41 | 0.74 | 19 | empty |
| 3 | 99 | 0.35 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2774 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 330 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5XCT · 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 5XCT · PDBe 5XCT
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.