MolNFT v1 · #121892 · protein + RNA

S. cerevisiae PRP43 in complex with RNA and adpnp

5I8Q · Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43: “S. cerevisiae PRP43 in complex with RNA and adpnp”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #121892 on GenesisL1: 3D…

PDB: 5I8Q
Type: protein + RNA
Length: 1,526 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43; RNA…
EC: 3.6.4.13
UniProt: P53131
Ligands: ANP, MG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (EC 3.6.4.13)	protein	752	41% helix, 17% strand	P53131
C	RNA (5'-R(PUPUPUPUPUPUPUPUP*U)-3')	rna	9	—	—
F	RNA (5'-R(PUPUPUPUPUPUPUPUPUPUPUPUP*U)-3')	rna	13	—	—

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, 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	946	0.89	0.91	118	empty
2	1199	0.88	0.90	127	empty
3	727	0.87	0.90	79	empty
4	323	0.79	0.90	39	empty
5	288	0.74	0.87	30	empty

Interfaces

3 interfaces between chains.

A–B · 2127 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 1840 Å² buried · 38 hydrogen bonds · protein-nucleic
A–C · 1433 Å² buried · 26 hydrogen bonds · protein-nucleic

Compared structures

5I8Q · S. cerevisiae Prp43 in complex with RNA and ADPNP · the same entry in another collection · chain A against A, TM-score 1.00
P53131 · AlphaFold monomer V2.0 prediction for pre-mRNA-splicing factor ATP- dependent RNA… · a predicted model of the same protein · chain A 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 P53131
Elsewhere: RCSB PDB 5I8Q · PDBe 5I8Q · UniProt P53131

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