MolNFT v1 · #164048 · protein

Crystal structure of PUF60 uhm domain in complex with 7,8 dimethoxyperphenazine

6SLO · THIOREDOXIN,POLY(U)-binding-splicing factor PUF60: “Crystal structure of PUF60 uhm domain in complex with 7,8 dimethoxyperphenazine”. X-ray diffraction, 2 ligands (LJT, MG), 10 pockets (best druggability 0.77). MolNFT v1 #164048 on…

PDB: 6SLO
Type: protein
Length: 846 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: THIOREDOXIN,POLY(U)-binding-splicing factor PUF60
UniProt: A0A064CXU8, Q9UHX1
Ligands: LJT, MG
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	THIOREDOXIN,POLY(U)-binding-splicing factor PUF60	protein	214	31% helix, 29% strand	A0A064CXU8, Q9UHX1
C, D	THIOREDOXIN,POLY(U)-binding-splicing factor PUF60	protein	209	31% helix, 30% strand	A0A064CXU8, Q9UHX1

Ligands and binding sites

LJT · 2-[4-[3-(8-chloranyl-2,3-dimethoxy-phenothiazin-10-yl) propyl]piperazin-1-yl]ethanol · ligand · 2 copies · chains C, D
MG · Magnesium ion · metal · 2 copies · chains A, D, C

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

Pockets

10 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	1173	0.77	0.79	149	empty
2	252	0.54	0.76	43	empty
3	134	0.50	0.79	21	empty
4	271	0.48	0.73	28	empty
5	82	0.44	0.80	14	LJT

Interfaces

6 interfaces between chains.

B–C · 1474 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1273 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 760 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 689 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 292 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6SLO · Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHX1 · AlphaFold monomer V2.0 prediction for POLY(U)-binding-splicing factor PUF60 (Q9UHX1) · a predicted model of the same protein · chain A against A, TM-score 0.51

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 A0A064CXU8
Every structure of UniProt Q9UHX1
Elsewhere: RCSB PDB 6SLO · PDBe 6SLO · UniProt A0A064CXU8 · UniProt Q9UHX1

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