2PAF: Lactose Repressor

Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state. Determined by X-ray diffraction at 3.5 Å resolution. Released 19 Jun 2007.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Escherichia coli
Chains: 2
Atoms: 4,068
Mol. weight: 58.08 kDa
Ligands: NPF
Released: 19 Jun 2007

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

Secondary structure: helices and β-sheets

2PAF contains 23 α-helices and 31 β-strands across 2 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: 10 helices, 16 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	105-108	4
β-strand	121-125	5	1
α-helix	130-140	11
β-strand	145-147	3	1
β-strand	158	1	1
β-strand	161	1	2
α-helix	163-177	15
β-strand	182-185	4	3
α-helix	192-207	16
β-strand	215-216	2	3
α-helix	222-233	12
β-strand	241-244	4	3
α-helix	247-259	13
α-helix	262-263	2
β-strand	264	1	4
β-strand	268	1	4
β-strand	269-271	3	3
β-strand	274	1	5
α-helix	277-281	5
β-strand	288-290	3	5
α-helix	293-307	15
β-strand	319	1	2
β-strand	322-324	3	5

Chain B: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	1
α-helix	74-87	14
α-helix	88-90	3
β-strand	93-98	6	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	163-175	13
β-strand	182-186	5	6
α-helix	192-206	15
β-strand	215-217	3	6
α-helix	222-227	6
α-helix	229-232	4
α-helix	233-235	3
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	285-287	3
β-strand	288-290	3	8
α-helix	293-309	17
β-strand	316-319	4	1
β-strand	322-324	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lactose operon repressor	A, B	protein	269	Escherichia coli	P03023 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2PAF_1 Lactose operon repressor (chains A, B)
LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSG
LIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQ
IALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTA
MLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSV
DRLLQLSQGQAVKGNQLLPVSLVKRKTTL

Ligands and cofactors

ID	Name	Formula	Copies
NPF	2-nitrophenyl beta-D-fucopyranoside	C12 H15 N O7	2

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
2PE5 3.5 Å, Crystal Structure of the Lac Repressor bound to ONPG in repressed state

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