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Crystal structure of truncated human crmp-4
Analyse Crystal structure of truncated human crmp-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CNS
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-like 3
- UniProt
- Q8IXW6
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase-like 3 | protein | 478 | 36% helix, 24% strand | Q8IXW6 |
| B | Dihydropyrimidinase-like 3 | protein | 477 | 36% helix, 24% strand | Q8IXW6 |
| C | Dihydropyrimidinase-like 3 | protein | 478 | 36% helix, 24% strand | Q8IXW6 |
| D | Dihydropyrimidinase-like 3 | protein | 479 | 36% helix, 24% strand | Q8IXW6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.85 | 0.87 | 92 | empty |
| 2 | 758 | 0.84 | 0.88 | 75 | empty |
| 3 | 206 | 0.68 | 0.86 | 35 | CL |
| 4 | 305 | 0.68 | 0.82 | 46 | CL |
| 5 | 248 | 0.67 | 0.84 | 44 | CL |
Interfaces
6 interfaces between chains.
- A–D · 1159 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1104 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1062 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CNS · Crystal structure of truncated human CRMP-4 · the same entry in another collection · chain A 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 Q8IXW6
- Elsewhere: RCSB PDB 4CNS · PDBe 4CNS · UniProt Q8IXW6
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