MolNFT v1 · #191082 · protein
Crystal structure of truncated aspartate transcarbamoylase from plasmodium falciparum in complex with bda-04
7ZP2 · Aspartate carbamoyltransferase: “Crystal structure of truncated aspartate transcarbamoylase from plasmodium falciparum in complex with bda-04”. X-ray diffraction, 3 ligands (EJG, NA, SO4), 19 pockets (best druggability 0.82). MolNFT…
- PDB
- 7ZP2
- Type
- protein
- Length
- 2,016 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase
- EC
- 2.1.3.2
- UniProt
- A0A5K1K910
- Ligands
- EJG, NA, SO4
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 328 | 43% helix, 16% strand | A0A5K1K910 |
| B, E | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 346 | 44% helix, 16% strand | A0A5K1K910 |
| C, F | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 334 | 43% helix, 16% strand | A0A5K1K910 |
Ligands and binding sites
- EJG · Tert-butyl N-[5-phenyl-3-(2-phenylethylcarbamoyl) thiophen-2-yl]carbamate · ligand · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.82 | 0.85 | 98 | NA, SO4 |
| 2 | 724 | 0.80 | 0.84 | 79 | SO4 |
| 3 | 336 | 0.79 | 0.90 | 41 | SO4, NA |
| 4 | 518 | 0.74 | 0.82 | 48 | empty |
| 5 | 480 | 0.73 | 0.82 | 48 | EJG |
Interfaces
9 interfaces between chains.
- A–C · 1016 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1009 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1002 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 975 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 948 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7ZP2 · Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum 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 A0A5K1K910
- Elsewhere: RCSB PDB 7ZP2 · PDBe 7ZP2 · UniProt A0A5K1K910
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