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Structure of mle RNA ADP ALF4 complex

Analyse Structure of mle RNA ADP ALF4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AOR
Type: protein + RNA
Length: 2,021 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dosage compensation regulator; 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
EC: 3.6.4.13
UniProt: P24785
Ligands: ADP, ALF, MG
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dosage compensation regulator (EC 3.6.4.13)	protein	1009	45% helix, 17% strand	P24785
B	Dosage compensation regulator (EC 3.6.4.13)	protein	992	46% helix, 17% strand	P24785
C, D	5'-R(UPUPUPUPUPUPUPUPUPUP*UP)-3'	rna	10	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, C, B

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.90	0.93	146	empty
2	1197	0.89	0.91	157	GOL
3	271	0.79	0.91	50	empty
4	514	0.79	0.86	66	ADP, MG, ALF
5	156	0.76	0.93	40	empty

Interfaces

3 interfaces between chains.

A–C · 1724 Å² buried · 38 hydrogen bonds · protein-nucleic
B–D · 1714 Å² buried · 38 hydrogen bonds · protein-nucleic
A–B · 717 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5AOR · Structure of MLE RNA ADP AlF4 complex · the same entry in another collection · chain A against A, TM-score 1.00
P24785 · AlphaFold monomer V2.0 prediction for dosage compensation regulator (P24785) · a predicted model of the same protein · chain B 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
Every structure of UniProt P24785
Elsewhere: RCSB PDB 5AOR · PDBe 5AOR · UniProt P24785

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