5GXB: LacY/Nanobody complex

crystal structure of a LacY/Nanobody complex. Determined by X-ray diffraction at 3.3 Å resolution. Released 26 Oct 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Escherichia coli (strain K12), Vicugna pacos
Chains: 2
Atoms: 4,121
Mol. weight: 63.31 kDa
Released: 26 Oct 2016

Explore 5GXB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GXB contains 32 α-helices and 11 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: 29 helices, 0 β-strands

Element	Residues	Length
α-helix	7-26	20
α-helix	30-32	3
α-helix	33-37	5
α-helix	45-69	25
α-helix	75-83	9
α-helix	84-86	3
α-helix	87-93	7
α-helix	104-110	7
α-helix	112-117	6
α-helix	122-132	11
α-helix	141-160	20
α-helix	161-163	3
α-helix	168-186	19
α-helix	210-213	4
α-helix	214-217	4
α-helix	220-228	9
α-helix	229-233	5
α-helix	234-239	6
α-helix	243-247	5
α-helix	248-250	3
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	352-356	5
α-helix	357-362	6
α-helix	364-376	13
α-helix	379-395	17

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	18-24	7	1
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
β-strand	93-98	6	3
α-helix	113-115	3
β-strand	118-119	2	3
β-strand	126-127	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lactose permease	A	protein	423	Escherichia coli (strain K12)	P02920 (AlphaFold model)
nanobody	B	protein	140	Vicugna pacos

Sequence of entity 1 (A), FASTA

>5GXB_1 Lactose permease (chains A)
MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQ
PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA
GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALIL
AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFD
QQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS
VRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL
AMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVAHHH
HHH

Sequence of entity 2 (B), FASTA

>5GXB_2 nanobody (chains B)
MQVQLVESGGRLVQAGDSLRLSCAASGRTFTTYLMGWFRQAPGKEREFVAAIRWSGGSTY
YADSVKGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAAAARPSYSGDYGYTEALRYDYW
GQGTQVTVSSHHHHHHEPEA

Primary citation

Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation. Jiang, X., Smirnova, I., Kasho, V. et al. Proc Natl Acad Sci U S A (2016) 113:12420-12425. DOI 10.1073/pnas.1615414113 · 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
4ZYR 3.31 Å, Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl…
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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