MolNFT v1 · #164024 · protein
Legionella effector ankx in complex with human RAB1B
6SKU · Phosphocholine transferase ankx: “Legionella effector ankx in complex with human RAB1B”. X-ray diffraction, 2 ligands (GDP, MG), 11 pockets (best druggability 0.80). MolNFT v1 #164024 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SKU
- Type
- protein
- Length
- 949 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphocholine transferase ankx; RAS-related protein rab-1B
- EC
- 2.7.1.-
- UniProt
- Q5ZXN6, Q9H0U4
- Ligands
- GDP, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphocholine transferase ankx (EC 2.7.1.-) | protein | 785 | 53% helix, 3% strand | Q5ZXN6 |
| B | RAS-related protein rab-1B | protein | 164 | 34% helix, 23% strand | Q9H0U4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.80 | 0.82 | 78 | empty |
| 2 | 1141 | 0.74 | 0.77 | 120 | GDP, MG |
| 3 | 357 | 0.67 | 0.81 | 32 | empty |
| 4 | 111 | 0.65 | 0.88 | 22 | empty |
| 5 | 326 | 0.58 | 0.76 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1966 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6SKU · Legionella effector AnkX in complex with human Rab1b · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZXN6 · AlphaFold monomer V2.0 prediction for phosphocholine transferase ankx (Q5ZXN6) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9H0U4 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1B (Q9H0U4) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q5ZXN6
- Every structure of UniProt Q9H0U4
- Elsewhere: RCSB PDB 6SKU · PDBe 6SKU · UniProt Q5ZXN6 · UniProt Q9H0U4
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