Research workbench
Crystal structure of E. COLI pure-mononucleotide complex.
Analyse Crystal structure of E. COLI pure-mononucleotide complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D7A
- Type
- protein
- Length
- 1,288 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylaminoimidazole carboxylase
- EC
- 4.1.1.21
- UniProt
- P09028
- Ligands
- AIR
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, L, M, N, O | Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) | protein | 161 | 48% helix, 14% strand | P09028 |
Ligands and binding sites
- AIR · 5-aminoimidazole ribonucleotide · ligand · 4 copies · chains A, O, B, N, C, M, D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.83 | 0.86 | 41 | empty |
| 2 | 448 | 0.67 | 0.79 | 62 | AIR |
| 3 | 281 | 0.61 | 0.79 | 35 | AIR |
| 4 | 272 | 0.61 | 0.80 | 34 | AIR |
| 5 | 320 | 0.60 | 0.78 | 42 | empty |
Interfaces
16 interfaces between chains.
- C–O · 1920 Ų buried · 25 hydrogen bonds · protein-protein
- D–N · 1915 Ų buried · 26 hydrogen bonds · protein-protein
- B–M · 1912 Ų buried · 27 hydrogen bonds · protein-protein
- A–L · 1907 Ų buried · 25 hydrogen bonds · protein-protein
- B–N · 1162 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 1D7A · Crystal structure of E. COLI pure-mononucleotide complex. · 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 P09028
- Elsewhere: RCSB PDB 1D7A · PDBe 1D7A · UniProt P09028
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