MolNFT v1 · #74267 · protein
Crystal structure of N5-carboxyaminoimidazole synthetase from staphylococcus aureus complexed with ADP
3ORQ · N5-carboxyaminoimidazole ribonucleotide synthetase: “Crystal structure of N5-carboxyaminoimidazole synthetase from staphylococcus aureus complexed with ADP”. X-ray diffraction, 3 ligands (ADP, POP, MG), 6 pockets (best druggability…
- PDB
- 3ORQ
- Type
- protein
- Length
- 739 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N5-carboxyaminoimidazole ribonucleotide synthetase
- EC
- 6.3.4.18
- UniProt
- A6QFS4
- Ligands
- ADP, POP, MG
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N5-carboxyaminoimidazole ribonucleotide synthetase (EC 6.3.4.18) | protein | 373 | 34% helix, 27% strand | A6QFS4 |
| B | N5-carboxyaminoimidazole ribonucleotide synthetase (EC 6.3.4.18) | protein | 366 | 37% helix, 27% strand | A6QFS4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.89 | 0.95 | 75 | empty |
| 2 | 728 | 0.76 | 0.81 | 64 | MG, ADP, POP |
| 3 | 529 | 0.62 | 0.75 | 63 | ADP, MG, GOL, POP |
| 4 | 105 | 0.49 | 0.81 | 22 | empty |
| 5 | 98 | 0.47 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1750 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3ORQ · Crystal Structure of N5-Carboxyaminoimidazole synthetase from Staphylococcus aureus… · 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 A6QFS4
- Elsewhere: RCSB PDB 3ORQ · PDBe 3ORQ · UniProt A6QFS4
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