Research workbench
Structure of T. thermophilus asprs in complex with 5'-O-(N-(L- aspartyl)-SULFAMOYL)CYTIDINE
Analyse Structure of T. thermophilus asprs in complex with 5'-O-(N-(L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HHX
- Type
- protein
- Length
- 1,154 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate--TRNA(ASP) ligase
- EC
- 6.1.1.12
- UniProt
- P36419
- Ligands
- G5N
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate--TRNA(ASP) ligase (EC 6.1.1.12) | protein | 574 | 33% helix, 25% strand | P36419 |
| B | Aspartate--TRNA(ASP) ligase (EC 6.1.1.12) | protein | 580 | 33% helix, 26% strand | P36419 |
Ligands and binding sites
- G5N · 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.97 | 20 | empty |
| 2 | 672 | 0.78 | 0.83 | 65 | G5N |
| 3 | 426 | 0.69 | 0.81 | 48 | G5N |
| 4 | 181 | 0.60 | 0.82 | 39 | empty |
| 5 | 51 | 0.52 | 0.88 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 5556 Ų buried · 84 hydrogen bonds · protein-protein
Compared structures
- 6HHX · Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine · the same entry in another collection · chain B against B, TM-score 1.00
- P36419 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP) ligase (P36419) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P36419
- Elsewhere: RCSB PDB 6HHX · PDBe 6HHX · UniProt P36419
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