MolNFT v1 · #153655 · protein
Crystal structure of aspartate transcarbamoylase from trypanosoma cruzi in complex with carbamoyl aspartate (ca) and phosphate (pi)
6JL4 · Aspartate carbamoyltransferase: “Crystal structure of aspartate transcarbamoylase from trypanosoma cruzi in complex with carbamoyl aspartate…”. X-ray diffraction, 4 ligands (ASP, NCD, CP), 20 pockets (best druggability 0.81). MolNFT…
- PDB
- 6JL4
- Type
- protein
- Length
- 1,900 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase
- EC
- 2.1.3.2
- UniProt
- O15636
- Ligands
- ASP, NCD, CP, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 307 | 42% helix, 15% strand | O15636 |
| B | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 319 | 46% helix, 14% strand | O15636 |
| C | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 323 | 45% helix, 14% strand | O15636 |
| D | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 319 | 43% helix, 14% strand | O15636 |
| E | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 310 | 41% helix, 15% strand | O15636 |
| F | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 322 | 42% helix, 14% strand | O15636 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 5 copies · chains B, C, A, D, E, F
- NCD · N-carbamoyl-L-aspartate · ligand · chains A, B
- CP · Phosphoric acid mono(formamide)ester · ligand · chains B, C
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.81 | 0.90 | 54 | empty |
| 2 | 359 | 0.81 | 0.90 | 47 | empty |
| 3 | 77 | 0.74 | 0.98 | 22 | ASP, PO4 |
| 4 | 1169 | 0.73 | 0.77 | 86 | empty |
| 5 | 66 | 0.72 | 0.98 | 20 | ASP, PO4 |
Interfaces
7 interfaces between chains.
- A–C · 1266 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1257 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1256 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1248 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1245 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6JL4 · Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with… · 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 O15636
- Elsewhere: RCSB PDB 6JL4 · PDBe 6JL4 · UniProt O15636
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