Research workbench
2.00 ångström resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrb) from yersinia pestis CO92
Analyse 2.00 ångström resolution crystal structure of a catalytic subunit of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LXM
- Type
- protein
- Length
- 849 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate carbamoyltransferase
- EC
- 2.1.3.2
- UniProt
- Q8ZB39
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 290 | 44% helix, 15% strand | Q8ZB39 |
| B | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 282 | 43% helix, 18% strand | Q8ZB39 |
| C | Aspartate carbamoyltransferase (EC 2.1.3.2) | protein | 277 | 42% helix, 17% strand | Q8ZB39 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.81 | 0.84 | 116 | empty |
| 2 | 245 | 0.61 | 0.81 | 45 | empty |
| 3 | 207 | 0.55 | 0.79 | 31 | empty |
| 4 | 213 | 0.54 | 0.78 | 44 | PG4 |
| 5 | 147 | 0.48 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 863 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 858 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 798 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3LXM · 2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZB39 · AlphaFold monomer V2.0 prediction for aspartate carbamoyltransferase (Q8ZB39) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8ZB39
- Elsewhere: RCSB PDB 3LXM · PDBe 3LXM · UniProt Q8ZB39
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