6C9W: Ligand bound LacY/Nanobody Complex

Crystal Structure of a ligand bound LacY/Nanobody Complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Aug 2018.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Escherichia coli (strain K12), Lama glama
Chains: 2
Atoms: 4,132
Mol. weight: 61 kDa
Ligands: BNG, 9PG
Released: 15 Aug 2018

Explore 6C9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C9W contains 29 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: 26 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-35	6
α-helix	45-69	25
α-helix	75-84	10
α-helix	87-89	3
α-helix	90-95	6
α-helix	96-100	5
α-helix	103-114	12
α-helix	115-119	5
α-helix	121-135	15
α-helix	140-162	23
α-helix	168-186	19
α-helix	210-214	5
α-helix	220-228	9
α-helix	229-233	5
α-helix	234-241	8
α-helix	243-248	6
α-helix	254-286	33
α-helix	289-308	20
α-helix	312-320	9
α-helix	322-340	19
α-helix	343-345	3
α-helix	346-349	4
α-helix	350-356	7
α-helix	357-375	19
α-helix	378-399	22

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-13	4	2
β-strand	20-23	4	1
β-strand	34-39	6	2
α-helix	43-45	3
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	69-73	5	1
β-strand	78-82	5	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	109-111	3
β-strand	112-115	4	2
β-strand	119-124	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lactose permease	A	protein	417	Escherichia coli (strain K12)	P02920 (AlphaFold model)
Nanobody9047	B	protein	125	Lama glama

Sequence of entity 1 (A), FASTA

>6C9W_1 Lactose permease (chains A)
MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQ
PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA
GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALIL
AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFD
QQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS
VRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL
AMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVA

Sequence of entity 2 (B), FASTA

>6C9W_2 Nanobody9047 (chains B)
VQLVESGGGLVQAGDSLRLSCAASGGTFSTFNMGWFRQDLGKEREFVAAIRWTGGRAYYG
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCARQGTNGGGYSEATSYNYWGQGTQV
TVSSH

Ligands and cofactors

ID	Name	Formula	Copies
BNG	nonyl beta-D-glucopyranoside	C15 H30 O6	1
9PG	4-nitrophenyl alpha-D-galactopyranoside	C12 H15 N O8	1

Primary citation

Crystal Structure of a ligand-bound LacY-Nanobody Complex. Kumar, H., Finer-Moore, J.S., Jiang, X. et al. Proc Natl Acad Sci U S A (2018) 115:8769-8774. DOI 10.1073/pnas.1801774115 · 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)
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
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

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