MolNFT v1 · #122174 · protein
Structure of the immune receptor CD33
5IHB · Myeloid cell surface antigen CD33: “Structure of the immune receptor CD33”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.54). MolNFT v1 #122174 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IHB
- 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
- Pockets
- 6 · 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, 45% strand | P20138 |
| B | Myeloid cell surface antigen CD33 | protein | 214 | 7% helix, 47% strand | P20138 |
| C | Myeloid cell surface antigen CD33 | protein | 212 | 9% helix, 45% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.54 | 0.76 | 46 | NAG |
| 2 | 215 | 0.51 | 0.76 | 34 | empty |
| 3 | 72 | 0.40 | 0.80 | 20 | empty |
| 4 | 113 | 0.38 | 0.74 | 23 | empty |
| 5 | 59 | 0.32 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–D · 825 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 679 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 427 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
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 5IHB · PDBe 5IHB · UniProt P20138
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