Research workbench
Escherichia COLI glutamine phosphoribosylpyrophosphate (prpp) amidotransferase complexed with mn-cprpp and 5-oxo- norleucine
Analyse Escherichia COLI glutamine phosphoribosylpyrophosphate (prpp) amidotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ECC
- Type
- protein
- Length
- 984 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine phosphoribosylpyrophosphate amidotransferase
- EC
- 2.4.2.14
- UniProt
- P00496
- Ligands
- ONL, PCP, MN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamine phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) | protein | 492 | 36% helix, 24% strand | P00496 |
Ligands and binding sites
- ONL · 5-oxo-L-norleucine · ligand · 2 copies · chains A, B
- PCP · 1-alpha-pyrophosphoryl-2-alpha,3-alpha-dihydroxy-4-beta-cyclopentane-methanol-5-phosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.82 | 0.97 | 40 | empty |
| 2 | 114 | 0.80 | 0.98 | 26 | MN, PCP |
| 3 | 115 | 0.80 | 0.98 | 26 | MN, PCP |
| 4 | 815 | 0.73 | 0.78 | 68 | empty |
| 5 | 136 | 0.57 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2095 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1ECC · Escherichia COLI glutamine phosphoribosylpyrophosphate (prpp) amidotransferase complexed… · 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 P00496
- Elsewhere: RCSB PDB 1ECC · PDBe 1ECC · UniProt P00496
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