MolNFT v1 · #68752 · protein
Crystal structure of carboxyaminoimidazole ribonucleotide synthase from asperigillus clavatus complexed with ATP
3K5H · Phosphoribosyl-aminoimidazole carboxylase: “Crystal structure of carboxyaminoimidazole ribonucleotide synthase from asperigillus clavatus complexed with…”. X-ray diffraction, 2 ligands (ATP, MG), 14 pockets (best druggability 0.85).…
- PDB
- 3K5H
- Type
- protein
- Length
- 1,524 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
- ATP, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phosphoribosyl-aminoimidazole carboxylase (EC 4.1.1.21) | protein | 382 | 35% helix, 26% strand | A1CII2 |
| B, D | Phosphoribosyl-aminoimidazole carboxylase (EC 4.1.1.21) | protein | 380 | 34% helix, 27% strand | A1CII2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.85 | 0.95 | 59 | empty |
| 2 | 299 | 0.84 | 0.94 | 51 | empty |
| 3 | 872 | 0.78 | 0.81 | 85 | ATP, MG |
| 4 | 1056 | 0.77 | 0.79 | 96 | ATP, MG |
| 5 | 553 | 0.75 | 0.82 | 61 | ATP, MG |
Interfaces
4 interfaces between chains.
- A–B · 1887 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1874 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3K5H · Crystal structure of carboxyaminoimidazole ribonucleotide synthase from asperigillus… · the same entry in another collection · chain B against B, 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 3K5H · PDBe 3K5H · UniProt A1CII2
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