MolNFT v1 · #70654 · protein

Branch recognition by SF3B14

3LQV · Pre-mRNA branch site protein P14: “Branch recognition by SF3B14”. X-ray diffraction, 1 ligand (ADE), 3 pockets (best druggability 0.75). MolNFT v1 #70654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LQV
Type: protein
Length: 304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA branch site protein P14; Splicing factor 3B subunit 1
UniProt: Q9Y3B4, O75533
Ligands: ADE
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA branch site protein P14	protein	113	35% helix, 20% strand	Q9Y3B4
B	Pre-mRNA branch site protein P14	protein	115	36% helix, 21% strand	Q9Y3B4
P	Splicing factor 3B subunit 1	protein	39	54% helix, 8% strand	O75533
Q	Splicing factor 3B subunit 1	protein	37	62% helix, 8% strand	O75533

Ligands and binding sites

ADE · Adenine · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	602	0.75	0.82	75	ADE
2	221	0.60	0.81	27	empty
3	127	0.44	0.77	22	ADE

Interfaces

4 interfaces between chains.

B–Q · 1461 Å² buried · 26 hydrogen bonds · protein-protein
A–P · 1330 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 533 Å² buried · 11 hydrogen bonds · protein-protein
B–P · 200 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3LQV · Branch Recognition by SF3b14 · the same entry in another collection · chain Q against Q, TM-score 1.00
Q9Y3B4 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 6 (Q9Y3B4) · a predicted model of the same protein · chain B against A, TM-score 0.99
O75533 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 1 (O75533) · a predicted model of the same protein · chain Q against A, TM-score 0.67

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 Q9Y3B4
Every structure of UniProt O75533
Elsewhere: RCSB PDB 3LQV · PDBe 3LQV · UniProt Q9Y3B4 · UniProt O75533

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