Research workbench

Structure of the standard kink turn hmkt-7 as stem loop bound with U1A and L7AE proteins

Analyse Structure of the standard kink turn hmkt-7 as stem loop bound with U1A and L7AE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FJ4
Type: protein + RNA
Length: 694 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U1 small nuclear ribonucleoprotein a; 50S ribosomal protein L7AE; Hmkt-7
UniProt: P09012, O29494
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	U1 small nuclear ribonucleoprotein a	protein	97	33% helix, 24% strand	P09012
C, G	50S ribosomal protein L7AE	protein	118	46% helix, 14% strand	O29494
D, H	Hmkt-7	rna	35	—	—

Pockets

10 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	780	0.70	0.77	89	empty
2	257	0.48	0.74	20	empty
3	52	0.44	0.83	15	empty
4	182	0.43	0.74	23	empty
5	84	0.43	0.80	22	empty

Interfaces

12 interfaces between chains.

E–H · 931 Å² buried · 33 hydrogen bonds · protein-nucleic
A–D · 896 Å² buried · 32 hydrogen bonds · protein-nucleic
C–D · 647 Å² buried · 24 hydrogen bonds · protein-nucleic
A–B · 616 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 613 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5FJ4 · Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins · the same entry in another collection · chain H against H, TM-score 1.00
O29494 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (O29494) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P09012
Every structure of UniProt O29494
Elsewhere: RCSB PDB 5FJ4 · PDBe 5FJ4 · UniProt P09012 · UniProt O29494

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.