Research workbench
Crystal structure of arnt from cupriavidus metallidurans in the apo state
Analyse Crystal structure of arnt from cupriavidus metallidurans in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EZM
- Type
- protein
- Length
- 537 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-amino-4-deoxy-L-arabinose transferase or related glycosyltransferases of pmt family
- EC
- 2.4.2.43
- UniProt
- Q1LDT6
- Ligands
- MPG, DSL, PC, ZN, CL, PO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-amino-4-deoxy-L-arabinose transferase or related glycosyltransferases of pmt family (EC 2.4.2.43) | protein | 537 | 69% helix, 5% strand | Q1LDT6 |
Ligands and binding sites
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 48 copies · chains A
- DSL · Mono-trans, octa-cis decaprenyl-phosphate · ligand · chains A
- PC · Phosphocholine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.70 | 0.76 | 67 | MPG, PC |
| 2 | 106 | 0.65 | 0.88 | 17 | DSL |
| 3 | 221 | 0.51 | 0.75 | 27 | MPG |
| 4 | 119 | 0.48 | 0.78 | 14 | MPG |
| 5 | 163 | 0.46 | 0.76 | 29 | empty |
Compared structures
- 5EZM · Crystal Structure of ArnT from Cupriavidus metallidurans in the apo state · 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 5EZM · PDBe 5EZM · UniProt Q1LDT6
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