Research workbench
High-resolution crystal structure of the human CD44 hyaluronan binding domain complex with undefined peptides
Analyse High-resolution crystal structure of the human CD44 hyaluronan binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PZ3
- Type
- protein
- Length
- 305 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD44 antigen; Undefined peptides modeled as aaav
- UniProt
- P16070
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD44 antigen | protein | 150 | 17% helix, 37% strand | P16070 |
| B | CD44 antigen | protein | 151 | 15% helix, 36% strand | P16070 |
| C | Undefined peptides modeled as aaav | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
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 | 472 | 0.70 | 0.81 | 57 | empty |
| 2 | 92 | 0.55 | 0.85 | 27 | EDO |
| 3 | 166 | 0.50 | 0.78 | 26 | MES |
| 4 | 55 | 0.34 | 0.78 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 847 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4PZ3 · High-resolution crystal structure of the human CD44 hyaluronan binding domain complex… · 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 A 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 4PZ3 · PDBe 4PZ3 · UniProt P16070
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