MolNFT v1 · #51391 · protein
Crystal structure of the coiled-coil domain of NDEL1 (A.A. 58 to 169)C
2V66 · Nuclear distribution protein nude-like 1: “Crystal structure of the coiled-coil domain of NDEL1 (A.A. 58 to 169)C”. X-ray diffraction, 1 ligand (HG), 1 pocket (best druggability 0.48). MolNFT v1 #51391 on GenesisL1: 3D structure…
- PDB
- 2V66
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear distribution protein nude-like 1
- UniProt
- Q9GZM8
- Ligands
- HG
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 96% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D, E | Nuclear distribution protein nude-like 1 | protein | 111 | 96% helix, 0% strand | Q9GZM8 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.48 | 0.84 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2071 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1913 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1852 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 1675 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 1495 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2V66 · Crystal Structure of the coiled-coil domain of Ndel1 (a.a. 58 to 169) C · the same entry in another collection · chain D against D, TM-score 1.00
- Q9GZM8 · AlphaFold monomer V2.0 prediction for nuclear distribution protein nude-like 1 (Q9GZM8) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q9GZM8
- Elsewhere: RCSB PDB 2V66 · PDBe 2V66 · UniProt Q9GZM8
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