Research workbench
Crystal structure of polyprenyl-phosphate N-acetyl hexosamine 1- phosphate transferase
Analyse Crystal structure of polyprenyl-phosphate N-acetyl hexosamine 1- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J72
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-N-acetylmuramoyl-pentapeptide-transferase
- EC
- 2.7.8.13
- UniProt
- O66465
- Ligands
- NI, MG
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 323 | 72% helix, 2% strand | O66465 |
| B | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 297 | 75% helix, 2% strand | O66465 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.87 | 0.88 | 72 | empty |
| 2 | 103 | 0.56 | 0.84 | 23 | empty |
| 3 | 100 | 0.54 | 0.84 | 24 | empty |
| 4 | 153 | 0.50 | 0.78 | 28 | empty |
| 5 | 137 | 0.48 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1638 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4J72 · Crystal Structure of polyprenyl-phosphate N-acetyl hexosamine 1-phosphate transferase · the same entry in another collection · chain A against A, TM-score 1.00
- O66465 · AlphaFold monomer V2.0 prediction for phospho-N-acetylmuramoyl- pentapeptide-transferase… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 O66465
- Elsewhere: RCSB PDB 4J72 · PDBe 4J72 · UniProt O66465
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