MolNFT v1 · #113495 · protein + RNA
Crystal structure of the ternary complex of agrobacterium radiobacter K84 AGNB2 leurs-tRNA-leuams
5AH5 · Leucine--tRNA ligase: “Crystal structure of the ternary complex of agrobacterium radiobacter K84 AGNB2 leurs-tRNA-leuams”. X-ray diffraction, 4 ligands (LSS, ZN, MN), 20 pockets (best druggability 0.74). MolNFT v1 #113495 on…
- PDB
- 5AH5
- Type
- protein + RNA
- Length
- 1,721 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine--tRNA ligase; TRNA-leu taa isoacceptor
- EC
- 6.1.1.4
- UniProt
- B9JQP8
- Ligands
- LSS, ZN, MN, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 789 | 41% helix, 19% strand | B9JQP8 |
| B | Leucine--tRNA ligase (EC 6.1.1.4) | protein | 771 | 41% helix, 20% strand | B9JQP8 |
| C | TRNA-leu taa isoacceptor | rna | 80 | — | — |
| D | TRNA-leu taa isoacceptor | rna | 81 | — | — |
Ligands and binding sites
- LSS · 5'-O-(L-leucylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.74 | 0.82 | 39 | empty |
| 2 | 822 | 0.74 | 0.79 | 45 | empty |
| 3 | 423 | 0.73 | 0.84 | 56 | empty |
| 4 | 370 | 0.71 | 0.83 | 38 | LSS |
| 5 | 327 | 0.70 | 0.83 | 37 | LSS |
Interfaces
5 interfaces between chains.
- B–D · 2252 Ų buried · 48 hydrogen bonds · protein-nucleic
- A–C · 2211 Ų buried · 47 hydrogen bonds · protein-nucleic
- A–B · 427 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–D · 107 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Compared structures
- 5AH5 · Crystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2… · the same entry in another collection · chain A against A, TM-score 1.00
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 B9JQP8
- Elsewhere: RCSB PDB 5AH5 · PDBe 5AH5 · UniProt B9JQP8
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