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Structure of a human PRP31-15.5K-U4 snrna complex

Analyse Structure of a human PRP31-15.5K-U4 snrna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OZB
Type: protein + RNA
Length: 796 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA comprising the 5' stem-loop RNA of U4SNRNA; U4/U6.U5 tri-snrnp 15.5 kda protein…
UniProt: P55769, Q8WWY3
Ligands: CA
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 5 distinct chains · 62% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, F	RNA comprising the 5' stem-loop RNA of U4SNRNA	rna	33	—	—
A	U4/U6.U5 tri-snrnp 15.5 kda protein	protein	126	45% helix, 16% strand	P55769
B	U4/U6 small nuclear ribonucleoprotein PRP31	protein	239	71% helix, 0% strand	Q8WWY3
D	U4/U6.U5 tri-snrnp 15.5 kda protein	protein	125	46% helix, 16% strand	P55769
E	U4/U6 small nuclear ribonucleoprotein PRP31	protein	240	69% helix, 0% strand	Q8WWY3

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B, E

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

Pockets

6 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	201	0.61	0.82	32	empty
2	133	0.47	0.79	19	empty
3	108	0.39	0.75	17	empty
4	119	0.38	0.74	17	empty
5	84	0.30	0.73	15	empty

Interfaces

7 interfaces between chains.

B–E · 1493 Å² buried · 15 hydrogen bonds · protein-protein
C–B · 692 Å² buried · 8 hydrogen bonds · protein-nucleic
F–D · 676 Å² buried · 24 hydrogen bonds · protein-nucleic
C–A · 671 Å² buried · 23 hydrogen bonds · protein-nucleic
F–E · 652 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

2OZB · Structure of a human Prp31-15.5K-U4 snRNA complex · the same entry in another collection · chain E against E, TM-score 1.00
P55769 · AlphaFold monomer V2.0 prediction for NHP2-like protein 1 (P55769) · a predicted model of the same protein · chain D against A, TM-score 0.98
Q8WWY3 · AlphaFold monomer V2.0 prediction for U4/U6 small nuclear ribonucleoprotein PRP31 (Q8WWY3) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P55769
Every structure of UniProt Q8WWY3
Elsewhere: RCSB PDB 2OZB · PDBe 2OZB · UniProt P55769 · UniProt Q8WWY3

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