Research workbench
Escherichia COLI glutamine phosphoribosylpyrophosphate (prpp) amidotransferase complexed with 2 gmp, 1 mg per subunit
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
- 1ECB
- Type
- protein
- Length
- 1,900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine phosphoribosylpyrophosphate amidotransferase
- EC
- 2.4.2.14
- UniProt
- P00496
- Ligands
- 5GP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) | protein | 475 | 33% helix, 25% strand | P00496 |
| B | Glutamine phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) | protein | 470 | 31% helix, 25% strand | P00496 |
| C | Glutamine phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) | protein | 482 | 33% helix, 24% strand | P00496 |
| D | Glutamine phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) | protein | 473 | 32% helix, 24% strand | P00496 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.86 | 0.87 | 101 | MG, 5GP |
| 2 | 1133 | 0.86 | 0.87 | 102 | MG, 5GP |
| 3 | 501 | 0.78 | 0.86 | 56 | empty |
| 4 | 1047 | 0.76 | 0.79 | 57 | empty |
| 5 | 967 | 0.76 | 0.79 | 62 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2316 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2296 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 914 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 913 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1ECB · 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 1ECB · PDBe 1ECB · UniProt P00496
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