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Crystal structure of arnt from cupriavidus metallidurans bound to undecaprenyl phosphate
Analyse Crystal structure of arnt from cupriavidus metallidurans bound to undecaprenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F15
- Type
- protein
- Length
- 541 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-amino-4-deoxy-L-arabinose (L-ARA4N) transferase
- UniProt
- Q1LDT6
- Ligands
- MPG, 5TR, CL, PO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-amino-4-deoxy-L-arabinose (L-ARA4N) transferase | protein | 541 | 70% helix, 5% strand | Q1LDT6 |
Ligands and binding sites
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 76 copies · chains A
- 5TR · [(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.72 | 0.78 | 78 | MPG |
| 2 | 92 | 0.65 | 0.90 | 18 | empty |
| 3 | 259 | 0.53 | 0.75 | 30 | MPG |
| 4 | 140 | 0.51 | 0.78 | 16 | MPG |
Compared structures
- 5F15 · Crystal Structure of ArnT from Cupriavidus metallidurans bound to Undecaprenyl phosphate · 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 Q1LDT6
- Elsewhere: RCSB PDB 5F15 · PDBe 5F15 · UniProt Q1LDT6
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