MolNFT v1 · #162177 · protein
Crystal structure of the SUN1-KASH4 6:6 complex
6R16 · Sun domain-containing protein 1: “Crystal structure of the SUN1-KASH4 6:6 complex”. X-ray diffraction, 2 ligands (K, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #162177 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6R16
- Type
- protein
- Length
- 1,316 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sun domain-containing protein 1; Nesprin-4
- UniProt
- O94901, Q8N205
- Ligands
- K, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sun domain-containing protein 1 | protein | 195 | 14% helix, 42% strand | O94901 |
| B, C, E, F | Sun domain-containing protein 1 | protein | 194 | 13% helix, 42% strand | O94901 |
| G, H | Nesprin-4 | protein | 26 | 0% helix, 19% strand | Q8N205 |
| I | Nesprin-4 | protein | 25 | 0% helix, 20% strand | Q8N205 |
| J | Nesprin-4 | protein | 27 | 0% helix, 19% strand | Q8N205 |
| K, L | Nesprin-4 | protein | 23 | 0% helix, 22% strand | Q8N205 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 3 copies · chains G, J, H, K, I, L
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, I, D, F, L, E, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.84 | 0.85 | 85 | empty |
| 2 | 1077 | 0.83 | 0.84 | 113 | EDO |
| 3 | 440 | 0.67 | 0.79 | 62 | empty |
| 4 | 277 | 0.62 | 0.80 | 42 | empty |
| 5 | 75 | 0.61 | 0.90 | 21 | empty |
Interfaces
34 interfaces between chains.
- C–J · 949 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 929 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 882 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 853 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 848 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6R16 · Crystal structure of the SUN1-KASH4 6:6 complex · the same entry in another collection · chain L against L, 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 O94901
- Every structure of UniProt Q8N205
- Elsewhere: RCSB PDB 6R16 · PDBe 6R16 · UniProt O94901 · UniProt Q8N205
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