MolNFT v1 · #29882 · protein + DNA

Crystal structure of PUT3/DNA complex

1ZME · DNA (5'- D(*AP*CP*GP*GP*GP*AP*AP*GP*CP*CP*AP*AP*CP*TP*CP*CP*…: “Crystal structure of PUT3/DNA complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.37). MolNFT v1 #29882 on GenesisL1: 3D structure, binding sites…

PDB: 1ZME
Type: protein + DNA
Length: 174 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*AP*CP*GP*GP*GP*AP*AP*GP*CP*CP*AP*AP*CP*TP*CP*CP*G)-3'); DNA…
UniProt: P25502
Ligands: ZN
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'- D(APCPGPGPGPAPAPGPCPCPAPAPCPTPCPCP*G)-3')	dna	17	—	—
B	DNA (5'-D(APCPGPGPAPGP(5IU) PTPGPGPCPTP(5IU)PCPCPCP*G)-3')	dna	17	—	—
C, D	Proline utilization transcription activator	protein	70	50% helix, 7% strand	P25502

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains C, D

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

Pockets

2 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	123	0.37	0.74	22	empty
2	87	0.33	0.74	14	empty

Interfaces

6 interfaces between chains.

C–D · 1129 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 765 Å² buried · 75 hydrogen bonds · nucleic-nucleic
A–D · 567 Å² buried · 8 hydrogen bonds · protein-nucleic
B–C · 533 Å² buried · 14 hydrogen bonds · protein-nucleic
B–D · 381 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

1ZME · Crystal structure of PUT3/DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
P25502 · AlphaFold monomer V2.0 prediction for proline utilization trans- activator (P25502) · a predicted model of the same protein · chain C against A, TM-score 0.50

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 P25502
Elsewhere: RCSB PDB 1ZME · PDBe 1ZME · UniProt P25502

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