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Crystal Structure of Human CRMP2 1-532, unmodified
Analyse Crystal Structure of Human CRMP2 1-532, unmodified in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JV9
- Type
- protein
- Length
- 1,947 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.26
- Source
- Homo sapiens
- Molecule
- Dihydropyrimidinase-related protein 2
- UniProt
- Q16555
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.26 · 4 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase-related protein 2 | protein | 486 | 35% helix, 23% strand | Q16555 |
| B | Dihydropyrimidinase-related protein 2 | protein | 495 | 35% helix, 23% strand | Q16555 |
| C | Dihydropyrimidinase-related protein 2 | protein | 483 | 36% helix, 23% strand | Q16555 |
| D | Dihydropyrimidinase-related protein 2 | protein | 483 | 36% helix, 23% strand | Q16555 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, D, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
- EDO · 1,2-ethanediol · additive · chains B, C
- PGE · Triethylene glycol · additive · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.86 | 0.89 | 82 | empty |
| 2 | 765 | 0.85 | 0.89 | 81 | empty |
| 3 | 366 | 0.72 | 0.84 | 33 | empty |
| 4 | 343 | 0.72 | 0.84 | 34 | empty |
| 5 | 258 | 0.66 | 0.82 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2156 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1647 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1256 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1236 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 6JV9 · PDBe 6JV9 · UniProt Q16555
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