MolNFT v1 · #139913 · protein
Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) from cryptococcus neoformans
5XU6 · Inositol-pentakisphosphate 2-kinase: “Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) from cryptococcus neoformans”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.76). MolNFT v1 #139913…
- PDB
- 5XU6
- Type
- protein
- Length
- 1,477 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-pentakisphosphate 2-kinase
- UniProt
- J9VKS8
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase | protein | 367 | 49% helix, 15% strand | J9VKS8 |
| B | Inositol-pentakisphosphate 2-kinase | protein | 354 | 46% helix, 16% strand | J9VKS8 |
| C | Inositol-pentakisphosphate 2-kinase | protein | 379 | 48% helix, 16% strand | J9VKS8 |
| D | Inositol-pentakisphosphate 2-kinase | protein | 377 | 47% helix, 17% strand | J9VKS8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.76 | 0.78 | 113 | empty |
| 2 | 594 | 0.72 | 0.80 | 53 | SO4 |
| 3 | 543 | 0.67 | 0.77 | 38 | SO4 |
| 4 | 62 | 0.62 | 0.91 | 21 | empty |
| 5 | 245 | 0.60 | 0.80 | 29 | SO4 |
Interfaces
3 interfaces between chains.
- C–D · 1030 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 432 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 5XU6 · Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) from… · 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 J9VKS8
- Elsewhere: RCSB PDB 5XU6 · PDBe 5XU6 · UniProt J9VKS8
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