Research workbench
Crystal structure of pyrrolysyl-tRNA synthetase-TRNA(PYL) complex from desulfitobacterium hafniense
Analyse Crystal structure of pyrrolysyl-tRNA synthetase-TRNA(PYL) complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZNI
- Type
- protein + RNA
- Length
- 702 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysyl-tRNA synthetase; Bacterial tRNA
- EC
- 6.1.1.26
- UniProt
- B0S4P3
- Ligands
- CA
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 279 | 35% helix, 20% strand | B0S4P3 |
| C, D | Bacterial tRNA | rna | 72 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.83 | 0.95 | 38 | empty |
| 2 | 914 | 0.81 | 0.84 | 65 | empty |
| 3 | 892 | 0.81 | 0.84 | 62 | empty |
| 4 | 468 | 0.77 | 0.85 | 33 | empty |
| 5 | 467 | 0.74 | 0.83 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2322 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1735 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–D · 1703 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–C · 307 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 291 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2ZNI · Crystal structure of Pyrrolysyl-tRNA synthetase-tRNA(Pyl) complex from Desulfitobacterium… · 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 B0S4P3
- Elsewhere: RCSB PDB 2ZNI · PDBe 2ZNI · UniProt B0S4P3
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