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NMR study of TRP repressor-mtr operator DNA complex

Analyse NMR study of TRP repressor-mtr operator DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CO0
Type: protein + DNA
Length: 250 residues
Chains: 4
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*GP*TP*AP*CP*TP*CP*GP*TP*GP*TP*AP*CP*TP*GP*GP*TP*AP *CP*A)-3'…
UniProt: P0A881
Ligands: TRP
Pockets: 7 · best druggability 0.75

Structure

solution nmr · 3 distinct chains · 59% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	5'-D(TPGPTPAPCPTPCPGPTPGPTPAPCPTPGPGPTPAP CPA)-3'	dna	20	—	—
F	5'-D(TPGPTPAPCPCPAPGPTPAPCPAPCPGPAPGPTPAP CPA)-3'	dna	20	—	—
A, B	TRP operon repressor	protein	105	59% helix, 0% strand	P0A881

Ligands and binding sites

TRP · Tryptophan · ligand · 2 copies · chains E, A, B, F

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.75	0.99	24	empty
2	100	0.73	0.95	21	TRP
3	121	0.57	0.83	18	empty
4	183	0.57	0.81	29	TRP
5	74	0.35	0.76	22	empty

Interfaces

6 interfaces between chains.

A–B · 2291 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 963 Å² buried · 119 hydrogen bonds · nucleic-nucleic
E–A · 515 Å² buried · 18 hydrogen bonds · protein-nucleic
F–A · 492 Å² buried · 15 hydrogen bonds · protein-nucleic
E–B · 360 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

1CO0 · NMR study of TRP repressor-mtr operator DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
P0A881 · AlphaFold monomer V2.0 prediction for TRP operon repressor (P0A881) · a predicted model of the same protein · chain A against A, TM-score 0.58

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 P0A881
Elsewhere: RCSB PDB 1CO0 · PDBe 1CO0 · UniProt P0A881

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