MolNFT v1 · #169135 · protein
Structure of phis Fab (SC44-8) in complex with phis mimetic peptide
6X1V · SC44-8 light chain: “Structure of phis Fab (SC44-8) in complex with phis mimetic peptide”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #169135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6X1V
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SC44-8 light chain; SC44-8 heavy chain; Aclyana-3-ptza peptide
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | SC44-8 light chain | protein | 215 | 8% helix, 57% strand | — |
| H | SC44-8 heavy chain | protein | 216 | 6% helix, 48% strand | — |
| D | Aclyana-3-ptza peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains L, H
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 | 596 | 0.64 | 0.75 | 57 | EDO |
| 2 | 89 | 0.37 | 0.76 | 22 | empty |
| 3 | 73 | 0.31 | 0.74 | 21 | empty |
| 4 | 56 | 0.29 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1877 Ų buried · 21 hydrogen bonds · protein-protein
- L–D · 319 Ų buried · 7 hydrogen bonds · protein-protein
- H–D · 284 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 6X1V · Structure of pHis Fab (SC44-8) in complex with pHis mimetic peptide · the same entry in another collection · chain L against L, 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 6X1V · PDBe 6X1V
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