Research workbench
Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin
Analyse Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XKL
- Type
- protein
- Length
- 217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Calcium-binding and coiled-coil domain-containing protein 2
- UniProt
- P62987, Q13137
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin | protein | 78 | 23% helix, 36% strand | P62987 |
| B | Calcium-binding and coiled-coil domain-containing protein 2 | protein | 30 | 33% helix, 20% strand | Q13137 |
| D | Calcium-binding and coiled-coil domain-containing protein 2 | protein | 31 | 32% helix, 19% strand | Q13137 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
- ACT · Acetate ion · additive · 4 copies · chains B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.55 | 0.74 | 52 | empty |
Interfaces
5 interfaces between chains.
- C–D · 562 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 188 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XKL · Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain A against A, TM-score 0.90
- Q13137 · AlphaFold monomer V2.0 prediction for calcium-binding and coiled-coil domain-containing… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P62987
- Every structure of UniProt Q13137
- Elsewhere: RCSB PDB 4XKL · PDBe 4XKL · UniProt P62987 · UniProt Q13137
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