MolNFT v1 · #12316 · RNA

The crystal structure of R(GGUCACAGCCC)2 metal free form

1KD5 · 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3': “The crystal structure of R(GGUCACAGCCC)2 metal free form”. X-ray diffraction, 1 pocket (best druggability 0.25). MolNFT v1 #12316 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1KD5
Type: RNA
Length: 22 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-R(GPGPUPCPAPCPAPGPCPCP*C)-3'	rna	11	—	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.25	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 547 Å² buried · 33 hydrogen bonds · nucleic-nucleic

Compared structures

1KD5 · The Crystal Structure of r(GGUCACAGCCC)2 metal free form · 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 1KD5 · PDBe 1KD5

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