MolNFT v1 · #88624 · protein
Phosphatidylinositol 4-kinase III beta in a complex with RAB11A-GTP- gamma-S and the rab-binding domain of FIP3
4D0M · Phosphatidylinositol 4-kinase beta: “Phosphatidylinositol 4-kinase III beta in a complex with RAB11A-GTP- gamma-S and the rab-binding domain of…”. X-ray diffraction, 3 ligands (093, GSP, MG), 20 pockets (best druggability 0.84).…
- PDB
- 4D0M
- Type
- protein
- Length
- 8,154 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-kinase beta; RAS-related protein rab-11A; RAB11 family-interacting…
- EC
- 2.7.1.67, 3.6.5.2
- UniProt
- Q9UBF8, P62491, O75154
- Ligands
- 093, GSP, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, I, M, O, Q, S, W, Y, c, g | Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) | protein | 470 | 55% helix, 9% strand | Q9UBF8 |
| B, D, H, J, N, P, R, T, X, Z, d, h | RAS-related protein rab-11A (EC 3.6.5.2) | protein | 173 | 36% helix, 27% strand | P62491 |
| E, K, U, a, e, i | RAB11 family-interacting protein 3 | protein | 41 | 83% helix, 2% strand | O75154 |
| F, L, V, b, f, j | RAB11 family-interacting protein 3 | protein | 32 | 91% helix, 0% strand | O75154 |
Ligands and binding sites
- 093 · N-(5-(4-chloro-3-(2-hydroxy-ethylsulfamoyl)- phenylthiazole-2-yl)-acetamide · ligand · 12 copies · chains A, C, G, I, M, O, Q, S, W, Y, c, g
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 12 copies · chains A, B, C, D, G, H, I, J, M, N, O, P, Q, R, S, T, W, X, Y, Z, c, d, g, h
- MG · Magnesium ion · metal · 12 copies · chains B, D, H, J, N, P, R, T, X, Z, d, h
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.84 | 0.85 | 105 | empty |
| 2 | 1096 | 0.84 | 0.85 | 107 | empty |
| 3 | 1073 | 0.84 | 0.85 | 101 | empty |
| 4 | 1060 | 0.83 | 0.84 | 121 | empty |
| 5 | 882 | 0.82 | 0.84 | 92 | empty |
Interfaces
106 interfaces between chains.
- W–c · 1011 Ų buried · 5 hydrogen bonds · protein-protein
- G–M · 954 Ų buried · 4 hydrogen bonds · protein-protein
- A–O · 937 Ų buried · 4 hydrogen bonds · protein-protein
- Y–g · 865 Ų buried · 5 hydrogen bonds · protein-protein
- C–S · 770 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
Compared structures
- 4D0M · Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the… · 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 Q9UBF8
- Every structure of UniProt P62491
- Every structure of UniProt O75154
- Elsewhere: RCSB PDB 4D0M · PDBe 4D0M · UniProt Q9UBF8 · UniProt P62491 · UniProt O75154
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