Research workbench
Structure of phis Fab (SC1-1) in complex with phis mimetic peptide
Analyse Structure of phis Fab (SC1-1) in complex with phis mimetic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1S
- Type
- protein
- Length
- 1,759 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SC1-1 heavy chain; SC1-1 light chain; NM23-1-ptza peptide
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C, E | SC1-1 heavy chain | protein | 221 | 7% helix, 50% strand | — |
| L, B, D, F | SC1-1 light chain | protein | 214 | 8% helix, 54% strand | — |
| A | SC1-1 heavy chain | protein | 220 | 7% helix, 51% strand | — |
| G, I, J, K | NM23-1-ptza peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains H, E, A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains H, L, A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.83 | 0.84 | 142 | SO4 |
| 2 | 518 | 0.64 | 0.76 | 57 | empty |
| 3 | 521 | 0.64 | 0.76 | 59 | MPD |
| 4 | 530 | 0.63 | 0.76 | 55 | empty |
| 5 | 427 | 0.61 | 0.76 | 50 | MPD |
Interfaces
22 interfaces between chains.
- A–B · 1967 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1965 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1923 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1919 Ų buried · 18 hydrogen bonds · protein-protein
- H–E · 407 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 8 modified (disulfide, cyclization, nonstandard).
Compared structures
- 6X1S · Structure of pHis Fab (SC1-1) 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 6X1S · PDBe 6X1S
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