Research workbench
Crystal structure of the aquifex reactor complex formed by dihydroorotase (H180A, H232A) with dihydroorotate and aspartate transcarbamoylase with N-(phosphonacetyl)-L-aspartate (pala)
Analyse Crystal structure of the aquifex reactor complex formed by dihydroorotase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BJH
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase; Aspartate carbamoyltransferase
- EC
- 3.5.2.3, 2.1.3.2
- UniProt
- O66990, O66726
- Ligands
- DOR, PAL, BA, ZN, PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 422 | 33% helix, 24% strand | O66990 |
| B | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 291 | 44% helix, 18% strand | O66726 |
Ligands and binding sites
- DOR · (4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid · ligand · chains A
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · chains B
- BA · Barium ion · metal · 3 copies · chains B
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.67 | 0.83 | 40 | EDO |
| 2 | 129 | 0.58 | 0.84 | 22 | PAL |
| 3 | 170 | 0.57 | 0.82 | 31 | DOR |
| 4 | 202 | 0.47 | 0.74 | 43 | EDO |
| 5 | 71 | 0.37 | 0.78 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4BJH · Crystal Structure of the Aquifex Reactor Complex Formed by Dihydroorotase (H180A, H232A)… · the same entry in another collection · chain A against A, TM-score 1.00
- O66990 · AlphaFold monomer V2.0 prediction for dihydroorotase (O66990) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O66726 · AlphaFold monomer V2.0 prediction for aspartate carbamoyltransferase (O66726) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O66990
- Every structure of UniProt O66726
- Elsewhere: RCSB PDB 4BJH · PDBe 4BJH · UniProt O66990 · UniProt O66726
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