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Crystal structure of the GAS5 gre mimic

Analyse Crystal structure of the GAS5 gre mimic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MCF
Type: RNA
Length: 78 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GAS5 grem fwd; GAS5 grem rev
Ligands: SO4
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	GAS5 grem fwd	rna	9	—	—
D	GAS5 grem rev	rna	11	—	—
A	GAS5 grem fwd	rna	8	—	—
B, F, H	GAS5 grem rev	rna	10	—	—
E, G	GAS5 grem fwd	rna	10	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	870	0.67	0.75	35	empty
2	76	0.27	0.72	10	empty
3	80	0.27	0.71	12	empty

Interfaces

14 interfaces between chains.

E–F · 460 Å² buried · 41 hydrogen bonds · nucleic-nucleic
C–D · 460 Å² buried · 39 hydrogen bonds · nucleic-nucleic
G–H · 459 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–B · 411 Å² buried · 35 hydrogen bonds · nucleic-nucleic
D–A · 114 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Compared structures

4MCF · Crystal structure of the Gas5 GRE Mimic · the same entry in another collection · chain C against C, 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
Elsewhere: RCSB PDB 4MCF · PDBe 4MCF

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