Research workbench
Crystal structure of human dihydropyrimidinease-like 2 (DPYSL2A) /collapsin response mediator protein (CRMP2 13-516) mutant Y479E/Y499E
Analyse Crystal structure of human dihydropyrimidinease-like 2 (DPYSL2A) /collapsin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MLE
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-related protein 2
- UniProt
- Q16555
- Ligands
- NI
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Dihydropyrimidinase-related protein 2 | protein | 468 | 35% helix, 24% strand | Q16555 |
| A | Dihydropyrimidinase-related protein 2 | protein | 472 | 34% helix, 24% strand | Q16555 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains C, A
- EDO · 1,2-ethanediol · additive · 10 copies · chains C, A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.67 | 0.82 | 47 | PEG, EDO |
| 2 | 540 | 0.67 | 0.78 | 34 | empty |
| 3 | 268 | 0.67 | 0.83 | 46 | empty |
| 4 | 204 | 0.61 | 0.82 | 23 | empty |
| 5 | 208 | 0.58 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- C–A · 1005 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5MLE · Crystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response… · the same entry in another collection · chain C against C, TM-score 1.00
- Q16555 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 2 (Q16555) · a predicted model of the same protein · chain C 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 Q16555
- Elsewhere: RCSB PDB 5MLE · PDBe 5MLE · UniProt Q16555
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