Research workbench
Crystal structure of human CRMP2 1-532, age-modified
Analyse Crystal structure of human CRMP2 1-532, age-modified in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JVB
- Type
- protein
- Length
- 1,940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-related protein 2
- UniProt
- Q16555
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydropyrimidinase-related protein 2 | protein | 482 | 36% helix, 23% strand | Q16555 |
| B | Dihydropyrimidinase-related protein 2 | protein | 491 | 36% helix, 22% strand | Q16555 |
| D | Dihydropyrimidinase-related protein 2 | protein | 485 | 36% helix, 22% strand | Q16555 |
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.85 | 0.88 | 90 | empty |
| 2 | 783 | 0.85 | 0.88 | 78 | empty |
| 3 | 870 | 0.74 | 0.78 | 104 | empty |
| 4 | 482 | 0.69 | 0.80 | 63 | empty |
| 5 | 231 | 0.65 | 0.83 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1225 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1200 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6JVB · Crystal Structure of Human CRMP2 1-532, AGE-modified · 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 C against A, TM-score 1.00
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 6JVB · PDBe 6JVB · UniProt Q16555
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