Research workbench
Crystal structure of the putative tRNA pseudouridine synthase D (trud) from methanosarcina mazei, northeast structural genomics target MAR1
Analyse Crystal structure of the putative tRNA pseudouridine synthase D (trud) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z2Z
- Type
- protein
- Length
- 874 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable tRNA pseudouridine synthase D
- EC
- 4.2.1.70
- UniProt
- Q8Q0M2
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable tRNA pseudouridine synthase D (EC 4.2.1.70) | protein | 437 | 36% helix, 19% strand | Q8Q0M2 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.76 | 0.81 | 60 | empty |
| 2 | 370 | 0.67 | 0.80 | 53 | empty |
| 3 | 221 | 0.57 | 0.79 | 35 | empty |
| 4 | 254 | 0.56 | 0.78 | 45 | empty |
| 5 | 138 | 0.48 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 906 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 1Z2Z · Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8Q0M2 · AlphaFold monomer V2.0 prediction for probable tRNA pseudouridine synthase D (Q8Q0M2) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q8Q0M2
- Elsewhere: RCSB PDB 1Z2Z · PDBe 1Z2Z · UniProt Q8Q0M2
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