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Co-crystals of the ternary complex containing a T-box stem I RNA, its cognate trnagly, and B. subtilis ybxf protein, treated by removing lithium sulfate and increasing PEG3350 concentration from 20% to 45% post crystallization

Analyse Co-crystals of the ternary complex containing a T-box stem I RNA, its cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TZZ
Type: protein + RNA
Length: 1,032 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome-associated protein L7AE-like; Engineered trnagly; T-box stem I RNA
UniProt: P46350
Ligands: MG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	Ribosome-associated protein L7AE-like	protein	81	42% helix, 19% strand	P46350
B, E, H, K	Engineered trnagly	rna	75	—	—
C, F, I, L	T-box stem I RNA	rna	102	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 29 copies · chains B, C, E, F, H, I, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.77	0.80	62	MG
2	1118	0.73	0.78	68	MG
3	961	0.71	0.77	35	MG
4	1081	0.70	0.76	45	empty
5	816	0.69	0.76	33	MG

Interfaces

17 interfaces between chains.

K–L · 860 Å² buried · 38 hydrogen bonds · nucleic-nucleic
H–I · 841 Å² buried · 38 hydrogen bonds · nucleic-nucleic
E–F · 823 Å² buried · 34 hydrogen bonds · nucleic-nucleic
B–C · 817 Å² buried · 33 hydrogen bonds · nucleic-nucleic
B–E · 585 Å² buried · 10 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

4TZZ · Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly… · the same entry in another collection · chain L against L, 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 P46350
Elsewhere: RCSB PDB 4TZZ · PDBe 4TZZ · UniProt P46350

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