3W7X: E. coli YgjK D324N

Name: PDB 3W7X: Crystal structure of E. coli YgjK D324N complexed with melibiose
Published: 2013-07-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Crystal structure of E. coli YgjK D324N complexed with melibiose. Determined by X-ray diffraction at 2.7 Å resolution. Released 17 Jul 2013.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Escherichia coli
Chains: 2
Atoms: 12,360
Mol. weight: 172.77 kDa
Ligands: CA
Released: 17 Jul 2013

Explore 3W7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3W7X contains 64 α-helices and 100 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, 50 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	12	1	1
β-strand	17-21	5	2
β-strand	27	1	2
β-strand	32	1	3
β-strand	39-40	2	4
β-strand	41	1	3
α-helix	42	1
β-strand	43	1	1
α-helix	44	1
β-strand	56-59	4	4
β-strand	64-78	15	4
β-strand	81-82	2	4
α-helix	83-84	2
β-strand	86-92	7	5
β-strand	95-101	7	5
β-strand	105-115	11	5
β-strand	118-127	10	5
β-strand	131-139	9	4
β-strand	142-146	5	2
β-strand	149-150	2	2
β-strand	155	1	2
α-helix	156-159	4
β-strand	166-170	5	5
β-strand	173-177	5	5
β-strand	181-183	3	6
β-strand	187-189	3	6
β-strand	194-199	6	5
β-strand	204-208	5	4
β-strand	211-218	8	4
β-strand	222-231	10	5
α-helix	234-249	16
α-helix	251-269	19
α-helix	277-292	16
β-strand	294-295	2	7
β-strand	298	1	8
β-strand	301	1	8
β-strand	305-306	2	7
β-strand	320	1	9
α-helix	322-332	11
α-helix	337-348	12
β-strand	369	1	10
β-strand	370	1	9
α-helix	374-375	2
α-helix	376-378	3
β-strand	386	1	10
α-helix	395-406	12
α-helix	409-429	21
β-strand	441-442	2	11
β-strand	449	1	12
α-helix	454	1
β-strand	455	1	12
β-strand	456-461	6	13
β-strand	464-469	6	13
α-helix	471-480	10
β-strand	485-487	3	13
α-helix	489-498	10
α-helix	504-506	3
α-helix	511-519	9
α-helix	524-527	4
β-strand	531-535	5	11
β-strand	541-546	6	11
β-strand	548-549	2	14
α-helix	551-570	20
α-helix	574-590	17
α-helix	591-595	5
β-strand	596-597	2	15
β-strand	602-603	2	15
β-strand	606-607	2	14
β-strand	621	1	14
α-helix	623-625	3
α-helix	629-632	4
α-helix	633-636	4
α-helix	642-652	11
β-strand	684-685	2	16
α-helix	686-698	13
α-helix	702-715	14
α-helix	724-725	2
β-strand	728-729	2	16
β-strand	736-737	2	16
α-helix	743-755	13

Chain B: 33 helices, 50 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	12	1	17
β-strand	17-21	5	18
β-strand	27	1	18
β-strand	32	1	19
β-strand	39-40	2	20
β-strand	41	1	19
β-strand	43	1	17
β-strand	56-59	4	20
β-strand	64-78	15	20
β-strand	81-82	2	20
α-helix	83-84	2
β-strand	86-92	7	21
β-strand	95-101	7	21
β-strand	105-115	11	21
β-strand	118-127	10	21
β-strand	131-139	9	20
β-strand	142-146	5	18
β-strand	150	1	18
β-strand	155	1	18
α-helix	156-159	4
β-strand	166-170	5	21
β-strand	173-177	5	21
β-strand	181-183	3	22
β-strand	187-189	3	22
β-strand	194-199	6	21
β-strand	204-208	5	20
β-strand	211-218	8	20
β-strand	222-231	10	21
α-helix	234-249	16
α-helix	251-269	19
α-helix	277-292	16
β-strand	294-295	2	23
β-strand	298	1	24
β-strand	301	1	24
β-strand	305-306	2	23
β-strand	320	1	25
α-helix	322-332	11
α-helix	337-348	12
α-helix	351-353	3
α-helix	360-362	3
β-strand	369	1	26
β-strand	370	1	25
α-helix	374-375	2
α-helix	376-378	3
β-strand	386	1	26
α-helix	395-406	12
α-helix	409-429	21
β-strand	441-442	2	27
β-strand	449	1	28
α-helix	454	1
β-strand	455	1	28
β-strand	456-460	5	29
β-strand	467-469	3	29
α-helix	471-480	10
β-strand	485-487	3	29
α-helix	489-498	10
α-helix	504-506	3
α-helix	511-518	8
α-helix	524-527	4
α-helix	528-530	3
β-strand	531-535	5	27
β-strand	541-546	6	27
β-strand	548-549	2	30
α-helix	551-570	20
α-helix	574-590	17
α-helix	591-595	5
β-strand	596-597	2	31
β-strand	602-603	2	31
β-strand	606-607	2	30
β-strand	621	1	30
α-helix	623-625	3
α-helix	629-632	4
α-helix	633-637	5
α-helix	642-652	11
α-helix	683	1
β-strand	684-685	2	32
α-helix	686-698	13
α-helix	702-715	14
α-helix	724-725	2
β-strand	728-729	2	32
β-strand	736-737	2	32
α-helix	743-755	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein YgjK	A, B	protein	760	Escherichia coli	P42592 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3W7X_1 Uncharacterized protein YgjK (chains A, B)
NADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLT
EEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSL
LETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGK
VRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKE
QMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGA
VKFNTVTPSVTGRWFSGNQTWPWNTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRP
QDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLV
AYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKKGDKEETQSGLNNYARVVEK
GQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGT
LLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTT
QFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNT
FVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLT
ADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity. Miyazaki, T., Ichikawa, M., Yokoi, G. et al. FEBS J (2013) 280:4560-4571. DOI 10.1111/febs.12424 · 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
6XUX 1.9 Å, Crystal structure of Megabody Mb-Nb207-cYgjK_NO
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…
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…

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