Research workbench
Crystal structure of spin labelled vcsiap R125A bound to an artificial peptide ligand.
Analyse Crystal structure of spin labelled vcsiap R125A bound to an artificial peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A5C
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialic acid-binding periplasmic protein siap
- UniProt
- Q9KR64
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sialic acid-binding periplasmic protein siap | protein | 316 | 51% helix, 21% strand | Q9KR64 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.84 | 0.90 | 77 | empty |
| 2 | 531 | 0.84 | 0.90 | 73 | empty |
| 3 | 63 | 0.51 | 0.86 | 18 | empty |
| 4 | 71 | 0.31 | 0.74 | 17 | empty |
| 5 | 58 | 0.29 | 0.74 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1695 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 7A5C · Crystal structure of spin labelled VcSiaP R125A bound to an artificial peptide ligand. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KR64 · AlphaFold monomer V2.0 prediction for sialic acid-binding periplasmic protein siap… · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9KR64
- Elsewhere: RCSB PDB 7A5C · PDBe 7A5C · UniProt Q9KR64
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