Research workbench
Crystal structure of human dihydropyrimidinease-like 2 (DPYSL2A) /collapsin response mediator protein (CRMP2) residues 13-516
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
- 5MKV
- Type
- protein
- Length
- 1,949 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-related protein 2
- UniProt
- Q16555
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase-related protein 2 | protein | 486 | 36% helix, 22% strand | Q16555 |
| B | Dihydropyrimidinase-related protein 2 | protein | 482 | 36% helix, 22% strand | Q16555 |
| C | Dihydropyrimidinase-related protein 2 | protein | 493 | 35% helix, 23% strand | Q16555 |
| D | Dihydropyrimidinase-related protein 2 | protein | 488 | 36% helix, 23% strand | Q16555 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.86 | 0.89 | 76 | EDO |
| 2 | 804 | 0.85 | 0.88 | 80 | EDO |
| 3 | 768 | 0.76 | 0.81 | 77 | empty |
| 4 | 694 | 0.76 | 0.82 | 65 | empty |
| 5 | 250 | 0.66 | 0.83 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2157 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1995 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1266 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MKV · Crystal Structure of Human Dihydropyrimidinease-like 2 (DPYSL2A)/Collapsin Response… · the same entry in another collection · chain D against D, TM-score 1.00
- Q16555 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 2 (Q16555) · 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 Q16555
- Elsewhere: RCSB PDB 5MKV · PDBe 5MKV · UniProt Q16555
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