Research workbench
Structure of phis Fab (SC50-3) in complex with phis mimetic peptide
Analyse Structure of phis Fab (SC50-3) 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
- 6X1T
- Type
- protein
- Length
- 2,639 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SC50-3 heavy chain; SC50-3 light chain; NM23-1-ptza peptide
- Ligands
- NAG, FUC, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A, C, E | SC50-3 heavy chain | protein | 221 | 7% helix, 51% strand | — |
| L, B, D, F, I | SC50-3 light chain | protein | 214 | 8% helix, 54% strand | — |
| G | SC50-3 heavy chain | protein | 217 | 7% helix, 49% strand | — |
| J | SC50-3 heavy chain | protein | 219 | 7% helix, 50% strand | — |
| K | SC50-3 light chain | protein | 212 | 8% helix, 53% strand | — |
| M, N | NM23-1-ptza peptide | protein | 6 | 0% helix, 0% strand | — |
| O, Q | NM23-1-ptza peptide | protein | 7 | 0% helix, 29% strand | — |
| P | NM23-1-ptza peptide | protein | 5 | 0% helix, 0% strand | — |
| R | NM23-1-ptza peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains H, L, A, B, C, D, E, F, G, I, J, K
- FUC · alpha-L-fucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 11 copies · chains H, L, A, B, C, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.83 | 0.85 | 99 | empty |
| 2 | 718 | 0.78 | 0.82 | 70 | empty |
| 3 | 897 | 0.78 | 0.80 | 102 | SO4 |
| 4 | 903 | 0.76 | 0.79 | 82 | empty |
| 5 | 542 | 0.72 | 0.81 | 66 | empty |
Interfaces
38 interfaces between chains.
- H–L · 2006 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1999 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1989 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1986 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1985 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 6 glycan, 6 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 6X1T · Structure of pHis Fab (SC50-3) 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 6X1T · PDBe 6X1T
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