MolNFT v1 · #82284 · protein
Crystal structure of GFP-WRNIP1 ubz domain fusion protein in complex with ubiquitin
3VHT · Green fluorescent protein: “Crystal structure of GFP-WRNIP1 ubz domain fusion protein in complex with ubiquitin”. X-ray diffraction, 2 ligands (CR2, ZN), 11 pockets (best druggability 0.72). MolNFT v1 #82284 on GenesisL1: 3D…
- PDB
- 3VHT
- Type
- protein
- Length
- 563 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; Green fluorescent PROTEIN,ATPASE WRNIP1; Ubiquitin
- EC
- 3.6.1.3
- UniProt
- Q96S55, P62983
- Ligands
- CR2, ZN
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 228 | 11% helix, 52% strand | — |
| B | Green fluorescent PROTEIN,ATPASE WRNIP1 (EC 3.6.1.3) | protein | 259 | 15% helix, 47% strand | Q96S55 |
| C | Ubiquitin | protein | 76 | 20% helix, 34% strand | P62983 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.72 | 0.98 | 25 | CR2 |
| 2 | 60 | 0.72 | 0.98 | 23 | CR2 |
| 3 | 101 | 0.56 | 0.85 | 27 | empty |
| 4 | 167 | 0.54 | 0.80 | 17 | empty |
| 5 | 212 | 0.48 | 0.75 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1020 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 715 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 3VHT · Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P62983 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62983) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q96S55 · AlphaFold monomer V2.0 prediction for ATPase WRNIP1 (Q96S55) · a predicted model of the same protein · chain B against A, TM-score 0.27
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 Q96S55
- Every structure of UniProt P62983
- Elsewhere: RCSB PDB 3VHT · PDBe 3VHT · UniProt Q96S55 · UniProt P62983
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