MolNFT v1 · #169134 · protein
Structure of phis Fab (SC39-4) in complex with phis mimetic peptide
6X1U · SC39-4 heavy chain: “Structure of phis Fab (SC39-4) in complex with phis mimetic peptide”. X-ray diffraction, 11 pockets (best druggability 0.62). MolNFT v1 #169134 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6X1U
- Type
- protein
- Length
- 862 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SC39-4 heavy chain; SC39-4 light chain; Aclyana-3-ptza peptide
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | SC39-4 heavy chain | protein | 214 | 6% helix, 50% strand | — |
| L, B | SC39-4 light chain | protein | 213 | 7% helix, 53% strand | — |
| D, C | Aclyana-3-ptza peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 5 copies · chains L, H, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.62 | 0.74 | 56 | empty |
| 2 | 519 | 0.61 | 0.75 | 51 | empty |
| 3 | 71 | 0.55 | 0.87 | 23 | empty |
| 4 | 82 | 0.52 | 0.85 | 28 | EDO |
| 5 | 118 | 0.44 | 0.78 | 26 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1805 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1766 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 234 Ų buried · 7 hydrogen bonds · protein-protein
- L–D · 230 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 190 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 modified (disulfide, cyclization, nonstandard).
Compared structures
- 6X1U · Structure of pHis Fab (SC39-4) in complex with pHis mimetic peptide · the same entry in another collection · chain H against H, 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 6X1U · PDBe 6X1U
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