MolNFT v1 · #86515 · protein
Crystal structure of truncated human crmp-5 soaked with zn
4B92 · Dihydropyrimidinase-related protein 5: “Crystal structure of truncated human crmp-5 soaked with zn”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.62). MolNFT v1 #86515 on GenesisL1: 3D structure, binding sites…
- PDB
- 4B92
- Type
- protein
- Length
- 951 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-related protein 5
- UniProt
- Q9BPU6
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase-related protein 5 | protein | 476 | 36% helix, 23% strand | Q9BPU6 |
| B | Dihydropyrimidinase-related protein 5 | protein | 475 | 37% helix, 22% strand | Q9BPU6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.62 | 0.78 | 43 | empty |
| 2 | 134 | 0.52 | 0.80 | 17 | empty |
| 3 | 143 | 0.49 | 0.78 | 20 | empty |
| 4 | 107 | 0.42 | 0.77 | 17 | empty |
| 5 | 73 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4B92 · Crystal structure of truncated human CRMP-5 soaked with Zn · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BPU6 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 5 (Q9BPU6) · a predicted model of the same protein · chain B 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 Q9BPU6
- Elsewhere: RCSB PDB 4B92 · PDBe 4B92 · UniProt Q9BPU6
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