Research workbench
Thermus thermophilus aspartyl-tRNA synthetase in complex with compound ASPS7HMDDA
Analyse Thermus thermophilus aspartyl-tRNA synthetase in complex with compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AP4
- Type
- protein
- Length
- 1,153 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
- Q5SKD2
- Ligands
- RSN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate--TRNA(ASP) ligase (EC 6.1.1.12) | protein | 573 | 33% helix, 26% strand | Q5SKD2 |
| B | Aspartate--TRNA(ASP) ligase (EC 6.1.1.12) | protein | 580 | 32% helix, 26% strand | Q5SKD2 |
Ligands and binding sites
- RSN · (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.97 | 21 | empty |
| 2 | 748 | 0.74 | 0.80 | 67 | RSN |
| 3 | 440 | 0.71 | 0.82 | 51 | RSN |
| 4 | 57 | 0.70 | 0.96 | 21 | empty |
| 5 | 60 | 0.68 | 0.95 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 5627 Ų buried · 89 hydrogen bonds · protein-protein
Compared structures
- 7AP4 · Thermus thermophilus Aspartyl-tRNA Synthetase in Complex with Compound AspS7HMDDA · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SKD2 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP) ligase (Q5SKD2) · 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 Q5SKD2
- Elsewhere: RCSB PDB 7AP4 · PDBe 7AP4 · UniProt Q5SKD2
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