MolNFT v1 · #18606 · protein + DNA

PU.1 ets domain-DNA complex

1PUE · DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)…: “PU.1 ets domain-DNA complex”. X-ray diffraction, 8 pockets (best druggability 0.54). MolNFT v1 #18606 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PUE
Type: protein + DNA
Length: 241 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)- 3'); DNA…
UniProt: P17433
Pockets: 8 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA (5'-D(APAPAPAPAPGPGPGPGPAPAPGPTPGPGPG)- 3')	dna	16	—	—
B, D	DNA (5'-D(TPCPCPCPAPCPTPTPCPCPCPCPTPTPTPT)- 3')	dna	16	—	—
E	Protein (transcription factor PU.1 (tf PU.1))	protein	88	42% helix, 18% strand	P17433
F	Protein (transcription factor PU.1 (tf PU.1))	protein	89	38% helix, 18% strand	P17433

Pockets

8 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	124	0.54	0.83	18	empty
2	141	0.53	0.81	18	empty
3	78	0.44	0.81	16	empty
4	64	0.42	0.81	13	empty
5	84	0.39	0.78	14	empty

Interfaces

6 interfaces between chains.

A–B · 690 Å² buried · 63 hydrogen bonds · nucleic-nucleic
C–D · 673 Å² buried · 69 hydrogen bonds · nucleic-nucleic
D–F · 601 Å² buried · 11 hydrogen bonds · protein-nucleic
B–E · 582 Å² buried · 10 hydrogen bonds · protein-nucleic
C–F · 536 Å² buried · 15 hydrogen bonds · protein-nucleic

Compared structures

1PUE · PU.1 ets domain-DNA complex · the same entry in another collection · chain F against F, TM-score 1.00
P17433 · AlphaFold monomer V2.0 prediction for transcription factor PU.1 (P17433) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 P17433
Elsewhere: RCSB PDB 1PUE · PDBe 1PUE · UniProt P17433

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