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Crystal structure of heterohexameric tusbcd proteins, which are crucial for the tRNA modification

Analyse Crystal structure of heterohexameric tusbcd proteins, which are crucial for the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 774 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 745 Å² buried · 10 hydrogen bonds · protein-protein
F–H · 738 Å² buried · 12 hydrogen bonds · protein-protein
E–I · 735 Å² 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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