MolNFT v1 · #48727 · protein
Crystal structure of oxalyl-CoA decarboxylase from escherichia COLI in complex with adenosine-5`-diphosphate
2Q28: “Crystal structure of oxalyl-CoA decarboxylase from escherichia COLI in complex with adenosine-5`-diphosphate”. X-ray diffraction, 4 ligands (TPP, ADP, MG), 7 pockets (best druggability 0.82). MolNFT v1 #48727 on GenesisL1: 3D…
- PDB
- 2Q28
- Type
- protein
- Length
- 1,100 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalyl-CoA decarboxylase
- EC
- 4.1.1.8
- UniProt
- P0AFI0
- Ligands
- TPP, ADP, MG, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxalyl-CoA decarboxylase (EC 4.1.1.8) | protein | 550 | 45% helix, 18% strand | P0AFI0 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.82 | 0.84 | 103 | ADP, EDO |
| 2 | 776 | 0.78 | 0.82 | 93 | TPP, ADP, EDO |
| 3 | 263 | 0.53 | 0.75 | 46 | empty |
| 4 | 67 | 0.50 | 0.85 | 15 | empty |
| 5 | 65 | 0.46 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1244 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2Q28 · Crystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AFI0 · AlphaFold monomer V2.0 prediction for oxalyl-CoA decarboxylase (P0AFI0) · a predicted model of the same protein · 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 P0AFI0
- Elsewhere: RCSB PDB 2Q28 · PDBe 2Q28 · UniProt P0AFI0
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