MolNFT v1 · #141165 · protein
Crystal structure of sialic acid binding protein from haemophilus ducreyi with NEU5GC
5YYB · Putative ABC transporter periplasmic binding protein: “Crystal structure of sialic acid binding protein from haemophilus ducreyi with NEU5GC”. X-ray diffraction, 1 ligand (NGE), 11 pockets (best druggability 0.74). MolNFT v1 #141165…
- 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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