3EZW: Glycerol kinase

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices. Determined by X-ray diffraction at 2.0 Å resolution. Released 4 Nov 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Escherichia coli
Chains: 8
Atoms: 32,916
Mol. weight: 475.86 kDa
Ligands: MG
Released: 4 Nov 2008

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

Secondary structure: helices and β-sheets

3EZW contains 175 α-helices and 242 β-strands across 8 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: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	15-21	7	1
β-strand	27-34	8	1
β-strand	38	1	2
β-strand	46-47	2	2
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	1
β-strand	86	1	2
β-strand	87-90	4	3
β-strand	96	1	3
β-strand	100-101	2	2
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-156	6
β-strand	160-163	4	3
α-helix	165-173	9
β-strand	180-182	3	4
α-helix	183-186	4
β-strand	192-193	2	5
β-strand	198-199	2	5
α-helix	201-207	7
α-helix	211-213	3
α-helix	214-215	2
β-strand	216-218	3	4
β-strand	221-227	7	1
β-strand	237-244	8	1
α-helix	245-252	8
β-strand	261-265	5	6
β-strand	269-274	6	6
β-strand	287-292	6	6
β-strand	298-306	9	6
α-helix	310-318	9
α-helix	329-333	5
β-strand	343-345	3	7
β-strand	348	1	8
β-strand	350	1	8
β-strand	351	1	9
β-strand	357	1	9
β-strand	362-367	6	7
α-helix	373-399	27
β-strand	405-407	3	10
β-strand	408-409	2	6
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	10
α-helix	438-450	13
α-helix	457-459	3
β-strand	466-470	5	10
α-helix	476-493	18
α-helix	498-499	2

Chain B: 19 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	11
β-strand	15-22	8	11
β-strand	27-34	8	11
β-strand	38	1	12
β-strand	46-47	2	12
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	11
β-strand	86	1	12
β-strand	87-90	4	13
β-strand	96	1	13
β-strand	100-101	2	12
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-156	6
β-strand	160-163	4	13
α-helix	165-173	9
β-strand	180-182	3	14
α-helix	183-186	4
β-strand	192-193	2	15
β-strand	198-199	2	15
α-helix	201-207	7
α-helix	211-213	3
β-strand	216-218	3	14
β-strand	221-228	8	11
β-strand	236-244	9	11
α-helix	245-252	8
β-strand	261-265	5	16
β-strand	269-274	6	16
β-strand	287-292	6	16
β-strand	298-306	9	16
α-helix	310-318	9
α-helix	329-333	5
β-strand	343-345	3	17
β-strand	348	1	18
β-strand	350	1	18
β-strand	351	1	19
β-strand	357	1	19
β-strand	362-367	6	17
α-helix	373-399	27
β-strand	405-407	3	20
β-strand	408	1	16
α-helix	416-426	11
β-strand	429-433	5	20
α-helix	438-451	14
α-helix	458-461	4
β-strand	467-470	4	20
α-helix	476-493	18
α-helix	498-499	2

Chain C: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	37
β-strand	15-21	7	37
β-strand	27-34	8	37
α-helix	36-37	2
β-strand	38	1	38
β-strand	46-47	2	38
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	37
β-strand	86	1	38
β-strand	87-90	4	39
β-strand	96	1	39
β-strand	100-101	2	38
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-157	7
β-strand	160-163	4	39
α-helix	165-173	9
β-strand	180-182	3	40
α-helix	183-187	5
β-strand	192-193	2	41
β-strand	198-199	2	41
α-helix	201-207	7
α-helix	211-213	3
α-helix	214-215	2
β-strand	216-218	3	40
β-strand	221-227	7	37
β-strand	237-244	8	37
α-helix	245-252	8
β-strand	261-265	5	42
β-strand	269-274	6	42
β-strand	287-292	6	42
β-strand	298-306	9	42
α-helix	310-318	9
α-helix	329-333	5
β-strand	343-345	3	43
β-strand	348	1	44
β-strand	350	1	44
β-strand	351	1	45
β-strand	357	1	45
β-strand	362-367	6	43
α-helix	373-399	27
β-strand	405-407	3	46
β-strand	408-409	2	42
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	46
α-helix	438-451	14
α-helix	457-462	6
β-strand	466-470	5	46
α-helix	476-493	18

Chain D: 23 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	47
β-strand	15-22	8	47
β-strand	27-34	8	47
β-strand	38	1	48
β-strand	46-47	2	48
α-helix	49-66	18
α-helix	71-73	3
β-strand	74-81	8	47
β-strand	86	1	48
β-strand	87-90	4	49
β-strand	96	1	49
β-strand	100-101	2	48
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-156	6
β-strand	160-163	4	49
α-helix	165-173	9
β-strand	180-182	3	50
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-193	2	51
β-strand	198-199	2	51
α-helix	201-206	6
α-helix	211-213	3
α-helix	214-215	2
β-strand	216-218	3	50
β-strand	221-227	7	47
β-strand	237-244	8	47
α-helix	245-252	8
β-strand	261-265	5	52
β-strand	269-274	6	52
α-helix	279-282	4
β-strand	287-292	6	52
β-strand	298-306	9	52
α-helix	310-318	9
α-helix	329-334	6
β-strand	343-345	3	53
β-strand	348	1	54
β-strand	350	1	54
β-strand	351	1	55
β-strand	357	1	55
β-strand	362-367	6	53
α-helix	373-399	27
α-helix	401-403	3
β-strand	405-409	5	52
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-432	4	52
α-helix	438-451	14
α-helix	457-460	4
β-strand	468-470	3	52
α-helix	476-493	18

Chain E: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	21
β-strand	15-22	8	21
β-strand	27-34	8	21
α-helix	36-37	2
β-strand	38	1	22
β-strand	46-47	2	22
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	21
β-strand	86	1	22
β-strand	87-90	4	23
β-strand	96	1	23
β-strand	100-101	2	22
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-157	7
β-strand	160-163	4	23
α-helix	165-173	9
β-strand	180-182	3	24
α-helix	183-186	4
β-strand	192-193	2	25
β-strand	198-199	2	25
α-helix	201-207	7
α-helix	211-213	3
α-helix	214-215	2
β-strand	216-218	3	24
β-strand	221-227	7	21
β-strand	237-244	8	21
α-helix	245-252	8
β-strand	261-265	5	26
β-strand	269-274	6	26
α-helix	279-282	4
β-strand	287-292	6	26
β-strand	298-306	9	26
α-helix	310-318	9
α-helix	329-333	5
β-strand	343-345	3	7
β-strand	348	1	27
β-strand	350	1	27
β-strand	351	1	28
β-strand	357	1	28
β-strand	362-367	6	7
α-helix	373-399	27
α-helix	401-403	3
β-strand	405-410	6	26
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	26
α-helix	438-451	14
α-helix	458-463	6
β-strand	466-470	5	26
α-helix	474-478	5
α-helix	479-493	15

Chain F: 24 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	56
β-strand	15-21	7	56
β-strand	27-34	8	56
β-strand	38	1	57
β-strand	46-47	2	57
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	56
β-strand	86-90	5	57
β-strand	96	1	57
α-helix	99	1
β-strand	100-101	2	57
α-helix	102	1
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-157	7
β-strand	160-164	5	57
α-helix	165-173	9
β-strand	180-182	3	58
α-helix	183-186	4
β-strand	192-193	2	59
β-strand	198-199	2	59
α-helix	201-207	7
α-helix	211-213	3
α-helix	214-215	2
β-strand	216-218	3	58
β-strand	221-227	7	56
α-helix	236	1
β-strand	237-244	8	56
α-helix	245-252	8
β-strand	261-265	5	60
β-strand	269-274	6	60
β-strand	287-292	6	60
β-strand	298-306	9	60
α-helix	310-318	9
α-helix	329-333	5
β-strand	343-345	3	53
β-strand	348	1	61
β-strand	350	1	61
β-strand	351	1	62
β-strand	357	1	62
β-strand	362-367	6	53
α-helix	373-399	27
β-strand	405-410	6	60
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	60
α-helix	438-451	14
α-helix	458-462	5
α-helix	464-465	2
β-strand	466-470	5	60
α-helix	476-493	18

Chain G: 22 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	29
β-strand	15-22	8	29
β-strand	27-34	8	29
β-strand	38	1	30
β-strand	46-47	2	30
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	29
β-strand	86	1	30
β-strand	87-90	4	31
β-strand	96	1	31
β-strand	100-101	2	30
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-156	6
β-strand	160-163	4	31
α-helix	165-173	9
β-strand	180-182	3	32
α-helix	183-186	4
β-strand	192-193	2	33
β-strand	198-199	2	33
α-helix	201-206	6
α-helix	211-213	3
α-helix	214-215	2
β-strand	216-218	3	32
β-strand	221-227	7	29
β-strand	237-244	8	29
α-helix	245-252	8
β-strand	261-265	5	34
β-strand	269-274	6	34
β-strand	287-292	6	34
β-strand	298-306	9	34
α-helix	310-318	9
α-helix	326-328	3
α-helix	329-333	5
β-strand	343-345	3	17
β-strand	348	1	35
β-strand	350	1	35
β-strand	351	1	36
β-strand	357	1	36
β-strand	362-367	6	17
α-helix	373-399	27
α-helix	401-403	3
β-strand	405-410	6	34
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	34
α-helix	438-450	13
α-helix	458-463	6
β-strand	466-470	5	34
α-helix	476-493	18

Chain H: 21 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	63
β-strand	15-21	7	63
β-strand	27-34	8	63
β-strand	38	1	64
β-strand	46-47	2	64
α-helix	49-67	19
α-helix	71-73	3
β-strand	74-81	8	63
β-strand	86	1	64
β-strand	87-90	4	65
β-strand	96	1	65
α-helix	99	1
β-strand	100-101	2	64
α-helix	102	1
α-helix	109-117	9
α-helix	121-128	8
α-helix	137-147	11
α-helix	151-156	6
β-strand	160-163	4	65
α-helix	165-173	9
β-strand	180-182	3	66
α-helix	183-187	5
β-strand	192-193	2	67
β-strand	198-199	2	67
α-helix	201-207	7
α-helix	211-213	3
β-strand	216-218	3	66
β-strand	221-227	7	63
β-strand	237-244	8	63
α-helix	245-252	8
β-strand	261-265	5	68
β-strand	269-274	6	68
β-strand	287-292	6	68
β-strand	298-306	9	68
α-helix	310-318	9
α-helix	329-333	5
β-strand	343-345	3	43
β-strand	348	1	69
β-strand	350	1	69
β-strand	351	1	70
β-strand	357	1	70
β-strand	362-367	6	43
α-helix	373-399	27
β-strand	406-410	5	68
α-helix	411-414	4
α-helix	416-426	11
β-strand	430-433	4	68
α-helix	438-451	14
α-helix	458-461	4
β-strand	466-470	5	68
α-helix	476-493	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycerol kinase	A, B, C, D, E, F, G, H	protein	526	Escherichia coli	P0A6F3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>3EZW_1 Glycerol kinase (chains A, B, C, D, E, F, G, H)
TEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTL
VEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGL
EDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHV
TDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIDGKGGTRIPIS
GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNY
ALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYA
RGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ
FQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERN
YRYAGWKKAVKRAMAWEEHDQLYTRASQPELAPEDPEDLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (GOL, CL, EDO) are not listed.

Primary citation

Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Anderson, M.J., DeLabarre, B., Raghunathan, A. et al. Biochemistry (2007) 46:5722-5731. DOI 10.1021/bi700096p · PubMed

Other PDB entries of the same protein (UniProt P0A6F3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1BU6 2.37 Å, Crystal structures of escherichia coli glycerol kinase and the mutant A65T in an…
1GLA 2.6 Å, Structure of the regulatory complex of escherichia coli iiiglc with glycerol kinase
1GLB 2.6 Å, Structure of the regulatory complex of escherichia coli iiiglc with glycerol kinase
1GLF 2.62 Å, Crystal structures of escherichia coli glycerol kinase and the mutant A65T in an…
1GLC 2.65 Å, Cation promoted association (CPA) of a regulatory and target protein is controlled by…
1GLD 2.93 Å, Cation promoted association (CPA) of a regulatory and target protein is controlled by…
1GLE 2.94 Å, Cation promoted association (CPA) of a regulatory and target protein is controlled by…
1BWF 3.0 Å, Escherichia coli glycerol kinase mutant with bound ATP analog showing substantial domain…
1GLJ 3.0 Å, Escherichia coli glycerol kinase mutant with bound ATP analog showing substantial domain…
1GLL 3.0 Å, Escherichia coli glycerol kinase mutant with bound ATP analog showing substantial domain…
1BOT 3.05 Å, Crystal structure of the complex between escherichia coli glycerol kinase and the…
1BO5 3.2 Å, Crystal structure of the complex between escherichia coli glycerol kinase and the…

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