MolNFT v1 · #101214 · protein
Crystal structure of SSPH1 lrr domain in complex PKN1 HR1B domain
4NKG · E3 ubiquitin-protein ligase SSPH1: “Crystal structure of SSPH1 lrr domain in complex PKN1 HR1B domain”. X-ray diffraction, 7 pockets (best druggability 0.61). MolNFT v1 #101214 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4NKG
- Type
- protein
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase SSPH1; SERINE/THREONINE-protein kinase N1
- EC
- 6.3.2.-, 2.7.11.13
- UniProt
- D0ZVG2, Q16512
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase SSPH1 (EC 6.3.2.-) | protein | 233 | 20% helix, 15% strand | D0ZVG2 |
| B | SERINE/THREONINE-protein kinase N1 (EC 2.7.11.13) | protein | 66 | 82% helix, 0% strand | Q16512 |
| C | E3 ubiquitin-protein ligase SSPH1 (EC 6.3.2.-) | protein | 230 | 19% helix, 16% strand | D0ZVG2 |
| D | SERINE/THREONINE-protein kinase N1 (EC 2.7.11.13) | protein | 65 | 86% helix, 0% strand | Q16512 |
Ligands and binding sites
- HEZ · Hexane-1,6-diol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.61 | 0.84 | 25 | empty |
| 2 | 62 | 0.42 | 0.81 | 16 | empty |
| 3 | 140 | 0.41 | 0.75 | 29 | empty |
| 4 | 104 | 0.38 | 0.75 | 16 | HEZ |
| 5 | 82 | 0.36 | 0.76 | 16 | HEZ |
Interfaces
3 interfaces between chains.
- A–B · 905 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 852 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4NKG · Crystal structure of SspH1 LRR domain in complex PKN1 HR1b domain · the same entry in another collection · chain D against D, TM-score 1.00
- D0ZVG2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase SSPH1 (D0ZVG2) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q16512 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase N1 (Q16512) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 D0ZVG2
- Every structure of UniProt Q16512
- Elsewhere: RCSB PDB 4NKG · PDBe 4NKG · UniProt D0ZVG2 · UniProt Q16512
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