MolNFT v1 · #33987 · protein
Crystal structure of heterohexameric tusbcd proteins, which are crucial for the tRNA modification
2D1P · Hypothetical UPF0163 protein yhen: “Crystal structure of heterohexameric tusbcd proteins, which are crucial for the tRNA modification”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.86). MolNFT v1 #33987 on…
- PDB
- 2D1P
- Type
- protein
- Length
- 1,030 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical UPF0163 protein yhen; Hypothetical UPF0116 protein yhem; Hypothetical…
- UniProt
- P45532, P45531, P45530
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Hypothetical UPF0163 protein yhen | protein | 130 | 42% helix, 22% strand | P45532 |
| B | Hypothetical UPF0116 protein yhem | protein | 119 | 39% helix, 18% strand | P45531 |
| C, F, I | Hypothetical protein yhel | protein | 95 | 39% helix, 22% strand | P45530 |
| E, H | Hypothetical UPF0116 protein yhem | protein | 118 | 40% helix, 19% strand | P45531 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 848 | 0.86 | 0.88 | 79 | empty |
| 2 | 130 | 0.78 | 0.96 | 25 | empty |
| 3 | 147 | 0.77 | 0.95 | 29 | empty |
| 4 | 677 | 0.71 | 0.78 | 67 | empty |
| 5 | 136 | 0.43 | 0.76 | 22 | empty |
Interfaces
18 interfaces between chains.
- D–G · 1001 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 745 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 738 Ų buried · 12 hydrogen bonds · protein-protein
- E–I · 735 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2D1P · crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA… · the same entry in another collection · chain I against I, TM-score 1.00
- P45530 · AlphaFold monomer V2.0 prediction for protein tusb (P45530) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P45531 · AlphaFold monomer V2.0 prediction for protein tusc (P45531) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P45532
- Every structure of UniProt P45531
- Every structure of UniProt P45530
- Elsewhere: RCSB PDB 2D1P · PDBe 2D1P · UniProt P45532 · UniProt P45531 · UniProt P45530
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