MolNFT v1 · #88301 · protein
Crystal structure of ligand-bound NAD1
4CQK · Flower-specific defensin: “Crystal structure of ligand-bound NAD1”. X-ray diffraction, 2 ligands (PIO, SO4), 8 pockets (best druggability 0.85). MolNFT v1 #88301 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CQK
- Type
- protein
- Length
- 658 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flower-specific defensin
- UniProt
- Q8GTM0
- Ligands
- PIO, SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Flower-specific defensin | protein | 47 | 21% helix, 28% strand | Q8GTM0 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 14 copies · chains A, C, G, J, B, H, D, N, E, F, K, I, L, M
- SO4 · Sulfate ion · ion · 20 copies · chains A, C, G, D, J, B, N, E, F, I, K, H, L, M
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, C, E, F, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.85 | 0.87 | 105 | empty |
| 2 | 549 | 0.80 | 0.87 | 71 | empty |
| 3 | 230 | 0.72 | 0.87 | 26 | empty |
| 4 | 50 | 0.58 | 0.91 | 19 | empty |
| 5 | 50 | 0.55 | 0.90 | 19 | empty |
Interfaces
25 interfaces between chains.
- E–N · 471 Ų buried · 16 hydrogen bonds · protein-protein
- D–G · 466 Ų buried · 16 hydrogen bonds · protein-protein
- I–K · 465 Ų buried · 16 hydrogen bonds · protein-protein
- F–H · 462 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide (disulfide).
Compared structures
- 4CQK · Crystal structure of ligand-bound NaD1 · the same entry in another collection · chain K against K, 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 Q8GTM0
- Elsewhere: RCSB PDB 4CQK · PDBe 4CQK · UniProt Q8GTM0
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