MolNFT v1 · #66690 · protein
Crystal structure of catalytic fragment of E. COLI alars G237A in complex with alasa
3HXZ · Alanyl-tRNA synthetase: “Crystal structure of catalytic fragment of E. COLI alars G237A in complex with alasa”. X-ray diffraction, 1 ligand (A5A), 20 pockets (best druggability 0.78). MolNFT v1 #66690 on GenesisL1: 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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