MolNFT v1 · #104050 · protein
High-resolution crystal structure of the human CD44 hyaluronan binding domain in new space group
4PZ4 · CD44 antigen: “High-resolution crystal structure of the human CD44 hyaluronan binding domain in new space group”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.75). MolNFT v1 #104050 on GenesisL1: 3D structure…
- PDB
- 4PZ4
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD44 antigen
- UniProt
- P16070
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD44 antigen | protein | 154 | 17% helix, 38% strand | P16070 |
| B | CD44 antigen | protein | 152 | 17% helix, 36% strand | P16070 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.75 | 0.80 | 95 | SO4, PEG, EDO, DMS |
| 2 | 67 | 0.36 | 0.78 | 15 | SO4 |
| 3 | 53 | 0.31 | 0.77 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 825 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4PZ4 · High-resolution crystal structure of the human CD44 hyaluronan binding domain in new… · the same entry in another collection · chain A against A, TM-score 1.00
- P16070 · AlphaFold monomer V2.0 prediction for CD44 antigen (P16070) · a predicted model of the same protein · chain B 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 P16070
- Elsewhere: RCSB PDB 4PZ4 · PDBe 4PZ4 · UniProt P16070
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