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Crystal structure analysis of a RNA helicase

Analyse Crystal structure analysis of a RNA helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LLM
Type: protein
Length: 470 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent RNA helicase a
EC: 3.6.1.-
UniProt: Q08211
Ligands: ADP, MN
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ATP-dependent RNA helicase a (EC 3.6.1.-)	protein	235	46% helix, 17% strand	Q08211

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
CAC · Cacodylate ion · additive · chains A
GOL · Glycerol · additive · chains B

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

Pockets

7 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	150	0.52	0.79	24	empty
2	108	0.48	0.80	21	empty
3	114	0.44	0.78	20	empty
4	74	0.37	0.77	16	empty
5	65	0.35	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 680 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

3LLM · Crystal Structure Analysis of a RNA Helicase · the same entry in another collection · chain A against A, TM-score 1.00
Q08211 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase a (Q08211) · a predicted model of the same protein · chain B 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 Q08211
Elsewhere: RCSB PDB 3LLM · PDBe 3LLM · UniProt Q08211

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