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Cooperativity and downstream binding in RNA replication

Analyse Cooperativity and downstream binding in RNA replication in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DHC
Type: RNA
Length: 56 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
Ligands: 5GP, MG
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R((LCC)P(LCC)P(LCA)P(LCG) PAPCPUPUPAPAPGPUPCPU)-3')	rna	14	—	—

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 8 copies · chains A, B, C, D
MG · Magnesium ion · metal · 15 copies · chains A, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	354	0.52	0.74	20	MG
2	360	0.51	0.73	21	MG

Interfaces

2 interfaces between chains.

C–D · 546 Å² buried · 43 hydrogen bonds · nucleic-nucleic
A–B · 544 Å² buried · 42 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 16 modified (nucleotide modification).

Compared structures

5DHC · Cooperativity and Downstream Binding in RNA Replication · the same entry in another collection · chain A against A, 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 5DHC · PDBe 5DHC

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