MolNFT v1 · #84313 · protein + RNA
Ternary complex of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and toxic moiety from agrocin 84 (TM84) in aminoacylation- like conformation
3ZGZ · Leucine--tRNA ligase: “Ternary complex of E. COLI leucyl-tRNA synthetase, TRNA(LEU) and toxic moiety from agrocin 84 (TM84) in…”. X-ray diffraction, 3 ligands (84T, MG, ZN), 19 pockets (best druggability 0.81). MolNFT v1 #84313 on…
- PDB
- 3ZGZ
- Type
- protein + RNA
- Length
- 1,884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase; TRNA-leu uaa isoacceptor
- EC
- 6.1.1.4
- UniProt
- P07813
- Ligands
- 84T, MG, ZN
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 860 | 39% helix, 22% strand | P07813 |
| B | TRNA-leu uaa isoacceptor | rna | 79 | — | — |
| D | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 867 | 37% helix, 22% strand | P07813 |
| E | TRNA-leu uaa isoacceptor | rna | 78 | — | — |
Ligands and binding sites
- 84T · [(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3-bis(oxidanyl)pentanoyl]phosphonamidic acid · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 7 copies · chains B, E
- ZN · Zinc ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.81 | 0.96 | 30 | 84T |
| 2 | 157 | 0.80 | 0.96 | 30 | 84T |
| 3 | 1011 | 0.78 | 0.80 | 80 | empty |
| 4 | 1135 | 0.77 | 0.79 | 98 | empty |
| 5 | 967 | 0.76 | 0.79 | 72 | empty |
Interfaces
3 interfaces between chains.
- D–E · 2936 Ų buried · 57 hydrogen bonds · protein-nucleic
- A–B · 2894 Ų buried · 56 hydrogen bonds · protein-nucleic
- A–D · 604 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZGZ · Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from… · the same entry in another collection · chain A against A, TM-score 1.00
- P07813 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase (P07813) · a predicted model of the same protein · chain D against A, TM-score 0.89
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 P07813
- Elsewhere: RCSB PDB 3ZGZ · PDBe 3ZGZ · UniProt P07813
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