6VBG: Galactoside permease

Lactose permease complex with thiodigalactoside and nanobody 9043. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Escherichia coli, Lama glama
Chains: 4
Atoms: 8,425
Mol. weight: 123.96 kDa
Ligands: BNG
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

6VBG contains 60 α-helices and 23 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: 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	45-70	26
α-helix	75-84	10
α-helix	87-90	4
α-helix	91-95	5
α-helix	96-101	6
α-helix	103-114	12
α-helix	115-119	5
α-helix	121-135	15
α-helix	140-161	22
α-helix	168-186	19
α-helix	210-214	5
α-helix	215-218	4
α-helix	220-228	9
α-helix	229-234	6
α-helix	235-239	5
α-helix	243-248	6
α-helix	255-285	31
α-helix	288-308	21
α-helix	312-320	9
α-helix	322-340	19
α-helix	343-345	3
α-helix	346-349	4
α-helix	350-357	8
α-helix	358-375	18
α-helix	378-399	22
α-helix	406-408	3

Chain B: 27 helices, 0 β-strands

Element	Residues	Length
α-helix	7-26	20
α-helix	30-32	3
α-helix	33-37	5
α-helix	42-70	29
α-helix	75-84	10
α-helix	87-90	4
α-helix	91-95	5
α-helix	96-101	6
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	234-239	6
α-helix	243-248	6
α-helix	254-285	32
α-helix	288-308	21
α-helix	312-340	29
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
α-helix	405-408	4

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	10-13	4	2
β-strand	18-26	9	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	69-73	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	104-107	4	2
β-strand	108	1	1
β-strand	111-116	6	2

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	10-13	4	4
β-strand	18-26	9	3
α-helix	29-31	3
β-strand	33-39	7	4
β-strand	46-51	6	4
β-strand	58-60	3	4
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-100	9	4
β-strand	103-107	5	4
β-strand	111-116	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Galactoside permease	A, B	protein	417	Escherichia coli	P02920 (AlphaFold model)
nanobody 9043	C, D	protein	121	Lama glama

Sequence of entity 1 (A, B), FASTA

>6VBG_1 Galactoside permease (chains A, B)
MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQ
PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA
GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALIL
AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFD
QQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS
VRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQL
AMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVA

Sequence of entity 2 (C, D), FASTA

>6VBG_2 nanobody 9043 (chains C, D)
QVQLVESGGGLVQAGDSLRLSCAASGRPFSNYAMGWFRQAPGKERERVASINWSGTDTDY
ADSVKGRFTISRDNAKRTLYLQMNTLKPEDTAVYYCAARVGVDYKYWGQGTQVTVSSHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
BNG	nonyl beta-D-glucopyranoside	C15 H30 O6	9

Primary citation

Diversity in kinetics correlated with structure in nano body-stabilized LacY. Kumar, H., Finer-Moore, J., Smirnova, I. et al. PLoS One (2020) 15:e0232846-e0232846. DOI 10.1371/journal.pone.0232846 · 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
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
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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