6XUX: Megabody Mb-Nb207-cYgjK_NO

Crystal structure of Megabody Mb-Nb207-cYgjK_NO. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Escherichia coli K-12
Chains: 1
Atoms: 7,672
Mol. weight: 101.66 kDa
Ligands: CA
Released: 13 Jan 2021

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

Secondary structure: helices and β-sheets

6XUX contains 35 α-helices and 61 β-strands across 1 chain. 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: 35 helices, 61 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-11	2	2
α-helix	12-13	2
β-strand	14-18	5	3
α-helix	20-29	10
α-helix	32-34	3
β-strand	35-36	2	3
α-helix	38-47	10
α-helix	53-55	3
α-helix	60-68	9
α-helix	73-76	4
β-strand	80-84	5	4
β-strand	90-95	6	4
β-strand	97-98	2	5
α-helix	100-119	20
α-helix	123-139	17
α-helix	140-144	5
β-strand	145-146	2	6
β-strand	151-152	2	6
β-strand	155-156	2	5
β-strand	170	1	5
α-helix	172-174	3
α-helix	178-181	4
α-helix	182-186	5
α-helix	191-201	11
β-strand	233-234	2	7
α-helix	235-247	13
α-helix	251-264	14
α-helix	273-274	2
β-strand	277-278	2	7
β-strand	285-286	2	7
α-helix	292-304	13
α-helix	328-330	3
β-strand	338	1	8
β-strand	343-347	5	9
β-strand	353	1	9
β-strand	358	1	10
β-strand	365-366	2	11
β-strand	367	1	10
β-strand	369	1	8
β-strand	382-386	5	11
β-strand	389-404	16	11
β-strand	407-408	2	11
β-strand	412-418	7	12
β-strand	421-427	7	12
β-strand	431-441	11	12
β-strand	444-453	10	12
β-strand	457-465	9	11
β-strand	468-472	5	9
β-strand	475-476	2	9
β-strand	481	1	9
α-helix	482-485	4
β-strand	492-496	5	12
β-strand	499-503	5	12
β-strand	508-509	2	13
β-strand	513-514	2	13
β-strand	520-525	6	12
β-strand	530-534	5	11
β-strand	537-544	8	11
β-strand	548-557	10	12
α-helix	560-575	16
α-helix	577-595	19
α-helix	603-619	17
β-strand	620-621	2	14
β-strand	624	1	15
β-strand	627	1	15
β-strand	631-632	2	14
β-strand	646	1	16
α-helix	648-658	11
α-helix	663-674	12
α-helix	686-688	3
β-strand	695	1	17
β-strand	696	1	16
α-helix	700-701	2
α-helix	702-704	3
β-strand	712	1	17
α-helix	721-732	12
α-helix	735-755	21
β-strand	767-769	3	4
β-strand	775	1	18
α-helix	780	1
β-strand	781	1	18
β-strand	782-786	5	3
α-helix	787-788	2
β-strand	789-796	8	1
β-strand	804-810	7	2
β-strand	817-823	7	2
β-strand	828-831	4	2
α-helix	833-835	3
β-strand	839-844	6	1
β-strand	849-854	6	1
α-helix	859-861	3
β-strand	863-870	8	2
α-helix	881-883	3
β-strand	886-887	2	2
β-strand	891-894	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody,Glucosidase YgjK,Glucosidase YgjK,Nanobody	A	protein	907	Escherichia coli K-12	P42592 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XUX_1 Nanobody,Glucosidase YgjK,Glucosidase YgjK,Nanobody (chains A)
QVQLVESGGGLVKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDK
EQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATIL
GKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEG
WSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWF
GLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGAQQGAPNFSWSAAHLYM
LYNDFFRKQASGGGSGGGGSGGGGSGNADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFD
LGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPG
ALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDK
TIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTS
KAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPD
ATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAH
FNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSL
AAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGE
MLFTVKKSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFT
ISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSSHHH
HHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Uchanski, T., Masiulis, S., Fischer, B. et al. Nat Methods (2021) 18:60-68. DOI 10.1038/s41592-020-01001-6 · PubMed

Other PDB entries of the same protein (UniProt P42592 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3W7T 1.5 Å, Escherichia coli K12 YgjK complexed with mannose
3D3I 1.78 Å, Crystal structural of Escherichia coli K12 YgjK, a glucosidase belonging to glycoside…
5CA3 1.8 Å, Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63 glycosidase…
3W7S 1.9 Å, Escherichia coli K12 YgjK complexed with glucose
3W7U 1.99 Å, Escherichia coli K12 YgjK complexed with galactose
3W7W 2.0 Å, Crystal structure of E. coli YgjK E727A complexed with 2-O-alpha-D-glucopyranosyl-alpha-D…
5GW7 2.2 Å, Crystal structure of the glycosynthase mutant E727A of Escherichia coli GH63 glycosidase…
3W7X 2.7 Å, Crystal structure of E. coli YgjK D324N complexed with melibiose
7Q1U 2.7 Å, Structure of Hedgehog acyltransferase (HHAT) in complex with megabody 177 bound to…
7PQQ 3.3 Å, Structure of thermostabilised human NTCP in complex with Megabody 91
8AFE 3.3 Å, Cryo-EM structure of crescentin filaments (stutter mutant, C1 symmetry and small box)
7Q6Z 3.59 Å, Structure of Hedgehog acyltransferase (HHAT) in complex with megabody 177 bound to…

Browse structure collections

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