MolNFT v1 · #29089 · protein
Crystal structure of kinase PIM1 in complex with AMP
1YXU · Proto-oncogene SERINE/THREONINE-protein kinase pim-1: “Crystal structure of kinase PIM1 in complex with AMP”. X-ray diffraction, 1 ligand (AMP), 14 pockets (best druggability 0.70). MolNFT v1 #29089 on GenesisL1: 3D structure…
- PDB
- 1YXU
- Type
- protein
- Length
- 1,091 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene SERINE/THREONINE-protein kinase pim-1
- EC
- 2.7.1.37
- UniProt
- P11309
- Ligands
- AMP
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Proto-oncogene SERINE/THREONINE-protein kinase pim-1 (EC 2.7.1.37) | protein | 273 | 37% helix, 23% strand | P11309 |
| C | Proto-oncogene SERINE/THREONINE-protein kinase pim-1 (EC 2.7.1.37) | protein | 272 | 38% helix, 24% strand | P11309 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.70 | 0.82 | 45 | AMP |
| 2 | 365 | 0.68 | 0.81 | 45 | AMP |
| 3 | 353 | 0.68 | 0.81 | 47 | AMP |
| 4 | 170 | 0.67 | 0.87 | 28 | empty |
| 5 | 201 | 0.65 | 0.84 | 28 | AMP |
Interfaces
3 interfaces between chains.
- B–C · 712 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 393 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1YXU · Crystal Structure of Kinase Pim1 in Complex with AMP · the same entry in another collection · chain A against A, 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 P11309
- Elsewhere: RCSB PDB 1YXU · PDBe 1YXU · UniProt P11309
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