MolNFT v1 · #151245 · protein
Structure of T. thermophilus asprs in complex with 5'-O-(N-(L- aspartyl)-SULFAMOYL)N3-methyluridine
6HHV · Aspartate--TRNA(ASP) ligase: “Structure of T. thermophilus asprs in complex with 5'-O-(N-(L- aspartyl)-SULFAMOYL)N3-methyluridine”. X-ray diffraction, 1 ligand (G5Q), 13 pockets (best druggability 0.80). MolNFT v1 #151245 on…
- PDB
- 6HHV
- 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
- G5Q
- 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 | 33% helix, 26% strand | P36419 |
| B | Aspartate--TRNA(ASP) ligase (EC 6.1.1.12) | protein | 580 | 32% helix, 26% strand | P36419 |
Ligands and binding sites
- G5Q · 5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.80 | 0.97 | 22 | empty |
| 2 | 652 | 0.78 | 0.84 | 72 | G5Q |
| 3 | 428 | 0.70 | 0.81 | 52 | G5Q |
| 4 | 77 | 0.63 | 0.90 | 22 | empty |
| 5 | 187 | 0.57 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 5555 Ų buried · 83 hydrogen bonds · protein-protein
Compared structures
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 6HHV · PDBe 6HHV · UniProt P36419
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.