MolNFT v1 · #132470 · protein

Pandda analysis group deposition -- AAR2/RNASEH in complex with fragment F2X-entry C05, dmso-free

5R0B · Pre-mRNA-splicing factor 8: “Pandda analysis group deposition -- AAR2/RNASEH in complex with fragment F2X-entry C05, dmso-free”. X-ray diffraction, 1 ligand (SY7), 6 pockets (best druggability 0.43). MolNFT v1 #132470 on GenesisL1…

PDB: 5R0B
Type: protein
Length: 537 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA-splicing factor 8; A1 cistron-splicing factor AAR2
UniProt: P33334, P32357
Ligands: SY7
Pockets: 6 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-splicing factor 8	protein	237	46% helix, 20% strand	P33334
B	A1 cistron-splicing factor AAR2	protein	300	45% helix, 18% strand	P32357

Ligands and binding sites

SY7 · 2-methoxy-4-[[(4~{S},5~{S})-2,4,5-tris(2-methoxypyridin-4-yl)imidazolidin-1-yl]methyl]pyridine · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	132	0.43	0.76	17	empty
2	114	0.37	0.73	18	empty
3	64	0.36	0.78	16	empty
4	87	0.35	0.75	11	empty
5	88	0.34	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 465 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5R0B · PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry C05… · the same entry in another collection · chain A against A, TM-score 1.00
P32357 · AlphaFold monomer V2.0 prediction for A1 cistron-splicing factor AAR2 (P32357) · 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 P33334
Every structure of UniProt P32357
Elsewhere: RCSB PDB 5R0B · PDBe 5R0B · UniProt P33334 · UniProt P32357

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