2PE5: Lac Repressor

Crystal Structure of the Lac Repressor bound to ONPG in repressed state. Determined by X-ray diffraction at 3.5 Å resolution. Released 18 Mar 2008.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: synthetic construct, Escherichia coli
Chains: 6
Atoms: 8,527
Mol. weight: 125.53 kDa
Ligands: 145
Released: 18 Mar 2008

Explore 2PE5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PE5 contains 43 α-helices and 50 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	17-25	9
α-helix	32-34	3
α-helix	35-44	10
α-helix	51-57	7
β-strand	63-69	7	1
α-helix	74-90	17
β-strand	93-99	7	1
α-helix	104-115	12
β-strand	122-125	4	1
α-helix	130-139	10
β-strand	145-147	3	1
β-strand	158-161	4	1
α-helix	163-176	14
β-strand	182-186	5	2
α-helix	192-206	15
β-strand	214-217	4	2
α-helix	222-233	12
β-strand	241-244	4	2
α-helix	247-260	14
β-strand	264	1	3
β-strand	268	1	3
β-strand	269-271	3	2
β-strand	274	1	4
α-helix	277-281	5
α-helix	285-286	2
β-strand	287	1	2
β-strand	288-290	3	4
α-helix	293-309	17
β-strand	316-319	4	1
β-strand	322-324	3	4

Chain B: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	17-24	8
α-helix	33-42	10
α-helix	51-57	7
β-strand	62-68	7	5
α-helix	74-89	16
β-strand	92-98	7	5
α-helix	104-116	13
β-strand	121-125	5	5
α-helix	130-139	10
β-strand	145-147	3	5
β-strand	158-161	4	5
α-helix	163-177	15
β-strand	182-186	5	6
α-helix	192-206	15
β-strand	215-217	3	6
α-helix	222-235	14
β-strand	241-244	4	6
α-helix	247-259	13
β-strand	264	1	7
β-strand	268	1	7
β-strand	269-271	3	6
β-strand	274	1	8
α-helix	277-281	5
α-helix	285-286	2
β-strand	287	1	6
β-strand	288-289	2	9
β-strand	290	1	8
α-helix	293-309	17
β-strand	316-319	4	5
β-strand	323-324	2	9

Chain C: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	17-23	7
α-helix	36-44	9
α-helix	51-56	6
β-strand	63-69	7	10
α-helix	74-90	17
β-strand	93-99	7	10
α-helix	104-116	13
β-strand	121-125	5	10
α-helix	130-139	10
β-strand	145-147	3	10
β-strand	158-161	4	10
α-helix	163-177	15
β-strand	182-186	5	11
α-helix	192-206	15
β-strand	215-217	3	11
α-helix	222-234	13
β-strand	241-244	4	11
α-helix	247-259	13
β-strand	264	1	12
β-strand	268	1	12
β-strand	269-271	3	11
β-strand	274	1	13
α-helix	278-281	4
α-helix	285-286	2
β-strand	287	1	11
β-strand	288-289	2	14
β-strand	290	1	13
α-helix	293-309	17
β-strand	316-319	4	10
β-strand	323-324	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(dapdapdtpdtpdgpdtpdgpdapdgpdcpdgpdcpdtpdcpdapdcpdapdapdtpdt)-3')	D, E, F	DNA	20	synthetic construct
Lactose operon repressor	A, B, C	protein	330	Escherichia coli	P03023 (AlphaFold model)

Sequence of entity 1 (D, E, F), FASTA

>2PE5_1 DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3') (chains D, E, F)
AATTGTGAGCGCTCACAATT

Sequence of entity 2 (A, B, C), FASTA

>2PE5_2 Lactose operon repressor (chains A, B, C)
KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQL
LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSG
LIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQ
IALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTA
MLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSV
DRLLQLSQGQAVKGNQLLPVSLVKRKTTLA

Ligands and cofactors

ID	Name	Formula	Copies
145	2-nitrophenyl beta-D-galactopyranoside	C12 H15 N O8	3

Primary citation

Structural analysis of lac repressor bound to allosteric effectors. Daber, R., Stayrook, S., Rosenberg, A. et al. J Mol Biol (2007) 370:609-619. DOI 10.1016/j.jmb.2007.04.028 · PubMed

Other PDB entries of the same protein (UniProt P03023 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GOH 1.1 Å, Homotetramic Antiparallel Coiled-Coil of 23-residues LacI C-terminal tetramerization helix
1JYE 1.7 Å, Structure of a Dimeric Lac Repressor with C-terminal Deletion and K84L Substitution
2P9H 2.0 Å, High resolution structure of the Lactose Repressor bound to IPTG
3EDC 2.1 Å, Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli…
1EFA 2.6 Å, Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf
1TLF 2.6 Å, Unprecedented quaternary structure of E. Coli lac repressor core tetramer: implications…
1LBI 2.7 Å, Lac repressor
4RZS 2.71 Å, Lac repressor engineered to bind sucralose, unliganded tetramer
1JYF 3.0 Å, Structure of the Dimeric Lac Repressor with an 11-residue C-terminal Deletion.
4RZT 3.1 Å, Lac repressor engineered to bind sucralose, sucralose-bound tetramer
1LBH 3.2 Å, Intact lactose operon repressor with gratuitous inducer iptg
2PAF 3.5 Å, Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state

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