MolNFT v1 · #101368 · protein
Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule
4NP3 · CD44 antigen: “Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule”. X-ray diffraction, 2 ligands (2L2, SO4), 2 pockets (best druggability 0.30). MolNFT v1 #101368 on GenesisL1: 3D structure…
- PDB
- 4NP3
- Type
- protein
- Length
- 150 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD44 antigen
- UniProt
- P15379
- Ligands
- 2L2, SO4
- Pockets
- 2 · best druggability 0.30
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD44 antigen | protein | 150 | 17% helix, 37% strand | P15379 |
Ligands and binding sites
- 2L2 · 2-[(4-methyl-1H-imidazol-5-yl)methyl]-1,2,3,4-tetrahydroisoquinolin-8-amine · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.30 | 0.76 | 14 | SO4 |
| 2 | 61 | 0.29 | 0.74 | 15 | 2L2 |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4NP3 · Crystal structure of the murine cd44 hyaluronan binding domain complex with a small… · the same entry in another collection · chain A against A, TM-score 1.00
- P15379 · AlphaFold monomer V2.0 prediction for CD44 antigen (P15379) · 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 P15379
- Elsewhere: RCSB PDB 4NP3 · PDBe 4NP3 · UniProt P15379
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