MolNFT v1 · #151246 · protein
Structure of T. thermophilus asprs in complex with 5'-O-(N-(L- aspartyl)-SULFAMOYL)URIDINE
6HHW · Aspartate--TRNA(ASP) ligase: “Structure of T. thermophilus asprs in complex with 5'-O-(N-(L- aspartyl)-SULFAMOYL)URIDINE”. X-ray diffraction, 1 ligand (G5H), 13 pockets (best druggability 0.80). MolNFT v1 #151246 on GenesisL1: 3D…
- PDB
- 6HHW
- 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
- G5H
- Pockets
- 13 · 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 | 34% helix, 25% strand | P36419 |
| B | Aspartate--TRNA(ASP) ligase (EC 6.1.1.12) | protein | 580 | 32% helix, 26% strand | P36419 |
Ligands and binding sites
- G5H · 5'-O-(N-(L-aspartyl)-sulfamoyl)uridine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.97 | 27 | empty |
| 2 | 719 | 0.78 | 0.83 | 76 | G5H |
| 3 | 426 | 0.69 | 0.81 | 50 | G5H |
| 4 | 184 | 0.60 | 0.82 | 39 | empty |
| 5 | 54 | 0.52 | 0.87 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 5541 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 6HHW · Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)uridine · the same entry in another collection · chain A against A, 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 6HHW · PDBe 6HHW · UniProt P36419
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