Research workbench
Crystal structure of two N-terminal domains of native siglec-5 in complex with 3'-sialyllactose
Analyse Crystal structure of two N-terminal domains of native siglec-5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZG3
- Type
- protein
- Length
- 210 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialic acid-binding ig-like lectin 5
- UniProt
- O15389
- Ligands
- BGC, GAL, SIA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialic acid-binding ig-like lectin 5 | protein | 210 | 7% helix, 40% strand | O15389 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.71 | 0.92 | 26 | empty |
| 2 | 59 | 0.35 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2ZG3 · Crystal Structure of Two N-terminal Domains of Native Siglec-5 in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O15389 · AlphaFold monomer V2.0 prediction for sialic acid-binding ig-like lectin 5 (O15389) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O15389
- Elsewhere: RCSB PDB 2ZG3 · PDBe 2ZG3 · UniProt O15389
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