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Structure of the dimeric lac REPRESSOR/OPERATOR O1/ONPF complex

Analyse Structure of the dimeric lac REPRESSOR/OPERATOR O1/ONPF complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JWL
Type: protein + DNA
Length: 955 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP* CP*AP*AP*TP*T)-3'…
UniProt: P03023
Ligands: NPF
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	5'-D(APGPAPAPTTPGPTPGPAPGPCPGPGPAPTPAPAP* CPAPAPTPT)-3'	dna	14	—	—
E	5'-D(TPAPAPTPTPGPTPTPAPTPCPCPGPCPTPCPAPCP APAPTPTP*C)-3'	dna	14	—	—
A, B	Lactose operon repressor	protein	329	44% helix, 18% strand	P03023
C	Lactose operon repressor	protein	269	42% helix, 21% strand	P03023

Ligands and binding sites

NPF · 2-nitrophenyl beta-D-fucopyranoside · ligand · 3 copies · chains A, B, C

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.82	0.83	117	NPF
2	325	0.75	0.87	45	NPF
3	784	0.75	0.80	90	empty
4	291	0.60	0.78	47	empty
5	325	0.59	0.77	51	empty

Interfaces

7 interfaces between chains.

A–B · 1878 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 632 Å² buried · 55 hydrogen bonds · nucleic-nucleic
D–B · 323 Å² buried · 2 hydrogen bonds · protein-nucleic
E–B · 289 Å² buried · 6 hydrogen bonds · protein-nucleic
B–C · 285 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1JWL · Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex · the same entry in another collection · chain E against E, TM-score 1.00
P03023 · AlphaFold monomer V2.0 prediction for lactose operon repressor (P03023) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 P03023
Elsewhere: RCSB PDB 1JWL · PDBe 1JWL · UniProt P03023

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