MolNFT v1 · #122798 · protein
Structure of the immune receptor CD33 in complex with 6'-sialyllactose
5J0B · Myeloid cell surface antigen CD33: “Structure of the immune receptor CD33 in complex with 6'-sialyllactose”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 4 pockets (best druggability 0.54). MolNFT v1 #122798 on GenesisL1: 3D…
- PDB
- 5J0B
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloid cell surface antigen CD33
- UniProt
- P20138
- Ligands
- NAG, GAL, SIA
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloid cell surface antigen CD33 | protein | 213 | 8% helix, 46% strand | P20138 |
| B | Myeloid cell surface antigen CD33 | protein | 214 | 6% helix, 47% strand | P20138 |
| C | Myeloid cell surface antigen CD33 | protein | 212 | 8% helix, 46% strand | P20138 |
| D | Myeloid cell surface antigen CD33 | protein | 209 | 6% helix, 46% strand | P20138 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.54 | 0.75 | 60 | empty |
| 2 | 248 | 0.53 | 0.76 | 38 | empty |
| 3 | 128 | 0.38 | 0.74 | 21 | empty |
| 4 | 68 | 0.33 | 0.76 | 13 | NAG |
Interfaces
4 interfaces between chains.
- A–D · 813 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 694 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 147 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5J0B · Structure of the immune receptor CD33 in complex with 6'-sialyllactose · the same entry in another collection · chain D against D, TM-score 1.00
- P20138 · AlphaFold monomer V2.0 prediction for myeloid cell surface antigen CD33 (P20138) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P20138
- Elsewhere: RCSB PDB 5J0B · PDBe 5J0B · UniProt P20138
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