Research workbench
Crystal structure of sialic acid binding protein from haemophilus ducreyi with NEU5GC
Analyse Crystal structure of sialic acid binding protein from haemophilus ducreyi with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YYB
- Type
- protein
- Length
- 964 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ABC transporter periplasmic binding protein
- UniProt
- Q7VL18
- Ligands
- NGE
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative ABC transporter periplasmic binding protein | protein | 482 | 33% helix, 24% strand | Q7VL18 |
Ligands and binding sites
- NGE · N-glycolyl-beta-neuraminic acid · ligand · 2 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.74 | 0.90 | 39 | NGE |
| 2 | 219 | 0.73 | 0.89 | 35 | NGE |
| 3 | 62 | 0.73 | 0.98 | 26 | empty |
| 4 | 61 | 0.71 | 0.97 | 27 | empty |
| 5 | 69 | 0.53 | 0.86 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 164 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5YYB · Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Gc · the same entry in another collection · chain A against A, 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
- Every structure of UniProt Q7VL18
- Elsewhere: RCSB PDB 5YYB · PDBe 5YYB · UniProt Q7VL18
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