Research workbench
The R state structure of E. COLI atcase with ATP and magnesium bound
Analyse The R state structure of E. COLI atcase with ATP and magnesium bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KH0
- Type
- protein
- Length
- 922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase; Aspartate carbamoyltransferase regulatory chain
- EC
- 2.1.3.2
- UniProt
- E8Y328, E8Y329
- Ligands
- ATP, PAL, ZN, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 310 | 41% helix, 15% strand | E8Y328 |
| B | Aspartate carbamoyltransferase regulatory chain (EC 2.1.3.2) | protein | 150 | 13% helix, 40% strand | E8Y329 |
| D | Aspartate carbamoyltransferase regulatory chain (EC 2.1.3.2) | protein | 152 | 16% helix, 36% strand | E8Y329 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains B, D
- PAL · N-(phosphonacetyl)-L-aspartic acid · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.72 | 0.80 | 55 | ATP |
| 2 | 109 | 0.61 | 0.87 | 23 | PAL |
| 3 | 108 | 0.60 | 0.87 | 22 | PAL |
| 4 | 110 | 0.39 | 0.75 | 22 | empty |
| 5 | 66 | 0.38 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1009 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 737 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4KH0 · The R state structure of E. coli ATCase with ATP and Magnesium bound · 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 E8Y328
- Every structure of UniProt E8Y329
- Elsewhere: RCSB PDB 4KH0 · PDBe 4KH0 · UniProt E8Y328 · UniProt E8Y329
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