MolNFT v1 · #88623 · protein
Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with RAB11A- GTP gammas
4D0L · Phosphatidylinositol 4-kinase beta: “Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with RAB11A- GTP gammas”. X-ray diffraction, 3 ligands (093, GSP, MG), 20 pockets (best druggability 0.76). MolNFT v1 #88623 on…
- PDB
- 4D0L
- Type
- protein
- Length
- 1,952 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-kinase beta; RAS-related protein rab-11A
- EC
- 2.7.1.67, 3.6.5.2
- UniProt
- Q9UBF8, P62491
- Ligands
- 093, GSP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) | protein | 470 | 54% helix, 9% strand | Q9UBF8 |
| B | RAS-related protein rab-11A (EC 3.6.5.2) | protein | 173 | 36% helix, 27% strand | P62491 |
| C | Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) | protein | 476 | 54% helix, 9% strand | Q9UBF8 |
| D, F | RAS-related protein rab-11A (EC 3.6.5.2) | protein | 177 | 36% helix, 28% strand | P62491 |
| E | Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) | protein | 479 | 54% helix, 10% strand | Q9UBF8 |
Ligands and binding sites
- 093 · N-(5-(4-chloro-3-(2-hydroxy-ethylsulfamoyl)- phenylthiazole-2-yl)-acetamide · ligand · 3 copies · chains A, C, E
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 3 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.76 | 0.82 | 77 | GSP, MG |
| 2 | 690 | 0.76 | 0.81 | 53 | empty |
| 3 | 663 | 0.75 | 0.81 | 74 | GSP |
| 4 | 841 | 0.73 | 0.78 | 63 | 093 |
| 5 | 780 | 0.73 | 0.78 | 64 | 093 |
Interfaces
9 interfaces between chains.
- A–D · 1071 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 963 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 625 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 597 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 589 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4D0L · Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UBF8 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase beta (Q9UBF8) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9UBF8
- Every structure of UniProt P62491
- Elsewhere: RCSB PDB 4D0L · PDBe 4D0L · UniProt Q9UBF8 · UniProt P62491
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