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Crystal structure of catalytic fragment of E. COLI alars G237A in complex with alasa
Analyse Crystal structure of catalytic fragment of E. COLI alars G237A in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HXZ
- Type
- protein
- Length
- 1,764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- EC
- 6.1.1.7
- UniProt
- P00957
- Ligands
- A5A
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 441 | 47% helix, 20% strand | P00957 |
Ligands and binding sites
- A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · 4 copies · chains A, B, C, D
- HED · 2-hydroxyethyl disulfide · additive · 8 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.78 | 0.80 | 83 | EPE |
| 2 | 1008 | 0.76 | 0.79 | 79 | EPE |
| 3 | 424 | 0.73 | 0.83 | 54 | A5A |
| 4 | 503 | 0.72 | 0.82 | 48 | empty |
| 5 | 418 | 0.72 | 0.83 | 52 | A5A |
Interfaces
5 interfaces between chains.
- A–C · 866 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 865 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 786 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 331 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3HXZ · Crystal Structure of catalytic fragment of E. coli AlaRS G237A in complex with AlaSA · the same entry in another collection · chain D against D, TM-score 1.00
- P00957 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (P00957) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P00957
- Elsewhere: RCSB PDB 3HXZ · PDBe 3HXZ · UniProt P00957
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