4ZYR: E. coli Lactose permease G46W/G262W

Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG). Determined by X-ray diffraction at 3.31 Å resolution. Released 29 Jul 2015.

Method: X-ray diffraction
Resolution: 3.31 Å
Organism: Escherichia coli (strain K12)
Chains: 2
Atoms: 6,241
Mol. weight: 94.79 kDa
Ligands: 9PG, BNG
Released: 29 Jul 2015

Explore 4ZYR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZYR contains 59 α-helices and 0 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: 31 helices, 0 β-strands

Element	Residues	Length
α-helix	7-26	20
α-helix	30-32	3
α-helix	33-37	5
α-helix	45-52	8
α-helix	60-69	10
α-helix	75-83	9
α-helix	84-86	3
α-helix	87-90	4
α-helix	91-95	5
α-helix	96-101	6
α-helix	108-111	4
α-helix	112-114	3
α-helix	115-119	5
α-helix	122-132	11
α-helix	141-160	20
α-helix	168-186	19
α-helix	210-213	4
α-helix	220-228	9
α-helix	229-233	5
α-helix	234-239	6
α-helix	243-248	6
α-helix	254-286	33
α-helix	288-305	18
α-helix	306-308	3
α-helix	312-340	29
α-helix	343-345	3
α-helix	346-351	6
α-helix	352-356	5
α-helix	357-361	5
α-helix	364-376	13
α-helix	378-395	18

Chain B: 28 helices, 0 β-strands

Element	Residues	Length
α-helix	7-24	18
α-helix	30-35	6
α-helix	45-52	8
α-helix	56-69	14
α-helix	75-83	9
α-helix	84-86	3
α-helix	87-89	3
α-helix	90-95	6
α-helix	96-100	5
α-helix	105-108	4
α-helix	112-114	3
α-helix	115-119	5
α-helix	122-132	11
α-helix	140-160	21
α-helix	168-186	19
α-helix	210-213	4
α-helix	220-228	9
α-helix	229-233	5
α-helix	234-239	6
α-helix	243-248	6
α-helix	254-286	33
α-helix	288-305	18
α-helix	312-340	29
α-helix	343-345	3
α-helix	346-351	6
α-helix	352-357	6
α-helix	358-373	16
α-helix	378-399	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lactose permease	A, B	protein	417	Escherichia coli (strain K12)	P02920 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4ZYR_1 Lactose permease (chains A, B)
MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQ
PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA
GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALIL
AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFD
QQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS
VRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL
AMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVA

Ligands and cofactors

ID	Name	Formula	Copies
9PG	4-nitrophenyl alpha-D-galactopyranoside	C12 H15 N O8	2
BNG	nonyl beta-D-glucopyranoside	C15 H30 O6	2

Primary citation

Structure of LacY with an alpha-substituted galactoside: Connecting the binding site to the protonation site. Kumar, H., Finer-Moore, J.S., Kaback, H.R. et al. Proc Natl Acad Sci U S A (2015) 112:9004-9009. DOI 10.1073/pnas.1509854112 · PubMed

Other PDB entries of the same protein (UniProt P02920 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9XOU 2.5 Å, CryoEM structure of LacY with Trimbody
6VBG 2.8 Å, Lactose permease complex with thiodigalactoside and nanobody 9043
2CFQ 2.95 Å, Sugar Free Lactose Permease at neutral pH
8YA0 2.97 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)
6C9W 3.0 Å, Crystal Structure of a ligand bound LacY/Nanobody Complex
8YA3 3.27 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT
8Y9Y 3.29 Å, Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)
2CFP 3.3 Å, Sugar Free Lactose Permease at acidic pH
5GXB 3.3 Å, crystal structure of a LacY/Nanobody complex
2Y5Y 3.38 Å, Crystal structure of LacY in complex with an affinity inactivator
1PV6 3.5 Å, Crystal structure of lactose permease
4OAA 3.5 Å, Crystal structure of E. coli lactose permease G46W,G262W bound to sugar

Browse structure collections

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