MolNFT v1 · #172532 · protein
Crystal structure of spin labelled vcsiap R125A bound to an artificial peptide ligand.
7A5C · Sialic acid-binding periplasmic protein siap: “Crystal structure of spin labelled vcsiap R125A bound to an artificial peptide ligand.”. X-ray diffraction, 5 pockets (best druggability 0.84). MolNFT v1 #172532 on GenesisL1: 3D…
- 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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