MolNFT v1 · #101209 · protein
Crystal structure of the cryptic polo box (CPB)OF zyg-1
4NKB · Probable SERINE/THREONINE-protein kinase zyg-1: “Crystal structure of the cryptic polo box (CPB)OF zyg-1”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.74). MolNFT v1 #101209 on GenesisL1: 3D structure, binding…
- PDB
- 4NKB
- Type
- protein
- Length
- 407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable SERINE/THREONINE-protein kinase zyg-1
- EC
- 2.7.11.1
- UniProt
- Q9GT24
- Ligands
- MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable SERINE/THREONINE-protein kinase zyg-1 (EC 2.7.11.1) | protein | 203 | 20% helix, 33% strand | Q9GT24 |
| B | Probable SERINE/THREONINE-protein kinase zyg-1 (EC 2.7.11.1) | protein | 204 | 22% helix, 33% strand | Q9GT24 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.74 | 0.77 | 81 | TRS |
| 2 | 79 | 0.44 | 0.81 | 18 | empty |
| 3 | 105 | 0.41 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4NKB · Crystal Structure of the cryptic polo box (CPB)of ZYG-1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GT24 · AlphaFold monomer V2.0 prediction for probable SERINE/THREONINE- protein kinase zyg-1… · a predicted model of the same protein · chain B against A, TM-score 0.76
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 Q9GT24
- Elsewhere: RCSB PDB 4NKB · PDBe 4NKB · UniProt Q9GT24
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