Research workbench
Crystal structure of RNase Z in complex with precursor TRNA(THR)
Analyse Crystal structure of RNase Z in complex with precursor TRNA(THR) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GCW
- Type
- protein + RNA
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease Z; TRNA(THR)
- EC
- 3.1.26.11
- UniProt
- P54548
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease Z (EC 3.1.26.11) | protein | 307 | 29% helix, 28% strand | P54548 |
| B | TRNA(THR) | rna | 55 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.71 | 0.76 | 50 | MES |
| 2 | 495 | 0.62 | 0.76 | 49 | empty |
| 3 | 86 | 0.42 | 0.80 | 12 | empty |
| 4 | 93 | 0.40 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1180 Ų buried · 30 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
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 P54548
- Elsewhere: RCSB PDB 4GCW · PDBe 4GCW · UniProt P54548
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