3EDC: Lactose operon repressor

Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli Lac-repressor Refined to 2.1 Resolution. Determined by X-ray diffraction at 2.1 Å resolution. Released 25 Nov 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Escherichia coli K12
Chains: 4
Atoms: 9,549
Mol. weight: 154.98 kDa
Ligands: HEZ
Released: 25 Nov 2008

Explore 3EDC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EDC contains 51 α-helices and 62 β-strands across 4 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: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	63-69	7	1
α-helix	74-90	17
β-strand	93-99	7	1
α-helix	104-116	13
β-strand	121-125	5	1
α-helix	130-139	10
β-strand	145-147	3	1
β-strand	158-161	4	1
α-helix	163-177	15
β-strand	182-186	5	2
α-helix	192-207	16
β-strand	214-217	4	2
α-helix	222-234	13
β-strand	241-244	4	2
α-helix	247-259	13
β-strand	264	1	3
β-strand	268	1	3
β-strand	269-274	6	2
α-helix	277-281	5
α-helix	285-286	2
β-strand	287-290	4	2
α-helix	293-308	16
β-strand	316-319	4	1
β-strand	322-324	3	2
α-helix	339-354	16

Chain B: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	63-69	7	1
α-helix	74-90	17
β-strand	93-99	7	1
α-helix	104-115	12
β-strand	121-125	5	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	4
α-helix	192-207	16
β-strand	214-217	4	4
α-helix	222-235	14
β-strand	241-244	4	4
α-helix	247-259	13
β-strand	264	1	5
β-strand	268	1	5
β-strand	269-274	6	4
α-helix	277-281	5
α-helix	285-286	2
β-strand	287-290	4	4
α-helix	293-308	16
β-strand	316-319	4	1
α-helix	320	1
β-strand	322-324	3	4
α-helix	331-333	3
α-helix	339-355	17

Chain C: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	6
α-helix	74-90	17
β-strand	93-98	6	6
α-helix	104-116	13
β-strand	121-125	5	6
α-helix	130-139	10
β-strand	145-147	3	6
β-strand	158-161	4	6
α-helix	163-177	15
β-strand	182-186	5	7
α-helix	187-188	2
α-helix	192-207	16
β-strand	214-217	4	7
α-helix	222-234	13
β-strand	241-244	4	7
α-helix	247-259	13
β-strand	264	1	8
β-strand	265	1	9
β-strand	268	1	8
β-strand	269-271	3	7
β-strand	274	1	10
α-helix	277-281	5
α-helix	285-286	2
β-strand	287	1	7
β-strand	288-290	3	10
α-helix	293-308	16
β-strand	316-319	4	6
α-helix	320	1
β-strand	322-324	3	10
β-strand	329	1	9
α-helix	332-333	2
α-helix	335-338	4
α-helix	339-354	16

Chain D: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	6
α-helix	74-90	17
β-strand	93-98	6	6
α-helix	99-100	2
α-helix	104-116	13
β-strand	121-125	5	6
α-helix	130-139	10
β-strand	145-147	3	6
β-strand	158-161	4	6
α-helix	163-177	15
β-strand	182-186	5	11
α-helix	192-207	16
β-strand	214-217	4	11
α-helix	222-234	13
β-strand	241-244	4	11
α-helix	247-259	13
β-strand	264	1	12
β-strand	265	1	13
β-strand	268	1	12
β-strand	269-274	6	11
α-helix	277-281	5
α-helix	285-286	2
β-strand	287-290	4	11
α-helix	293-308	16
β-strand	316-319	4	6
β-strand	322-324	3	11
β-strand	329	1	13
α-helix	339-354	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lactose operon repressor	A, B, C, D	protein	360	Escherichia coli K12	P03023 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3EDC_1 Lactose operon repressor (chains A, B, C, D)
MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ
SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS
GLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQ
QIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPT
AMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTS
VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ

Ligands and cofactors

ID	Name	Formula	Copies
HEZ	Hexane-1,6-diol	C6 H14 O2	4

Primary citation

Crystal structure of a 1.6-hexanediol bound tetrameric form of Escherichia coli lac-repressor refined to 2.1 A resolution. Stenberg, K.A.E., Vihinen, M. Proteins (2009) 75:748-759. DOI 10.1002/prot.22284 · 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
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
2PE5 3.5 Å, Crystal Structure of the Lac Repressor bound to ONPG in repressed state

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