Research workbench
Crystal structure of N5-carboxyaminoimidazole synthase from aspergillus clavatus in complex with ADP and 5-aminoimadazole ribonucleotide
Analyse Crystal structure of N5-carboxyaminoimidazole synthase from aspergillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K5I
- Type
- protein
- Length
- 1,512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyl-aminoimidazole carboxylase
- EC
- 4.1.1.21
- UniProt
- A1CII2
- Ligands
- ADP, AIR, MG, NA
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyl-aminoimidazole carboxylase (EC 4.1.1.21) | protein | 381 | 33% helix, 27% strand | A1CII2 |
| B | Phosphoribosyl-aminoimidazole carboxylase (EC 4.1.1.21) | protein | 376 | 34% helix, 27% strand | A1CII2 |
| C | Phosphoribosyl-aminoimidazole carboxylase (EC 4.1.1.21) | protein | 382 | 34% helix, 26% strand | A1CII2 |
| D | Phosphoribosyl-aminoimidazole carboxylase (EC 4.1.1.21) | protein | 373 | 35% helix, 28% strand | A1CII2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- AIR · 5-aminoimidazole ribonucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.84 | 0.95 | 50 | empty |
| 2 | 277 | 0.84 | 0.95 | 54 | empty |
| 3 | 363 | 0.76 | 0.87 | 50 | ADP, MG, AIR |
| 4 | 1043 | 0.76 | 0.79 | 104 | empty |
| 5 | 455 | 0.76 | 0.85 | 68 | NA, ADP, MG, AIR |
Interfaces
5 interfaces between chains.
- A–B · 1949 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1919 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 482 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3K5I · Crystal structure of N5-carboxyaminoimidazole synthase from aspergillus clavatus in… · 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 A1CII2
- Elsewhere: RCSB PDB 3K5I · PDBe 3K5I · UniProt A1CII2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.