1BWF: Glycerol kinase

Escherichia coli glycerol kinase mutant with bound ATP analog showing substantial domain motion. Determined by X-ray diffraction at 3.0 Å resolution. Released 18 May 1999.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Escherichia coli
Chains: 2
Atoms: 7,900
Mol. weight: 113.84 kDa
Ligands: ATF, MG
Released: 18 May 1999

Explore 1BWF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BWF contains 46 α-helices and 63 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 O: 20 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	10
β-strand	15-21	7	10
β-strand	27-34	8	10
β-strand	38	1	11
β-strand	46-47	2	11
α-helix	49-65	17
β-strand	74-81	8	10
β-strand	86-90	5	11
β-strand	95-96	2	11
β-strand	100-101	2	11
α-helix	109-118	10
α-helix	121-127	7
α-helix	137-147	11
α-helix	152-156	5
β-strand	160-164	5	11
α-helix	165-173	9
β-strand	180-182	3	12
α-helix	183-186	4
β-strand	193	1	13
β-strand	198	1	13
α-helix	201-206	6
α-helix	211-213	3
β-strand	216-218	3	12
β-strand	221	1	14
β-strand	226-228	3	15
β-strand	236-238	3	15
β-strand	241	1	14
β-strand	243-244	2	10
α-helix	245-252	8
β-strand	261-265	5	16
β-strand	269-276	8	16
α-helix	280-282	3
β-strand	287-292	6	16
β-strand	298-306	9	16
α-helix	310-315	6
α-helix	316-320	5
α-helix	329-333	5
β-strand	343-345	3	8
β-strand	348	1	17
β-strand	350	1	17
β-strand	352	1	16
β-strand	362-367	6	8
α-helix	373-395	23
α-helix	396-400	5
β-strand	405-409	5	16
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	16
α-helix	438-450	13
β-strand	466-470	5	16
α-helix	476-493	18

Chain Y: 26 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	15	1	2
β-strand	16-22	7	1
β-strand	27-31	5	1
β-strand	34	1	2
β-strand	38	1	3
β-strand	46-47	2	3
α-helix	49-65	17
β-strand	74-81	8	1
β-strand	86-90	5	3
β-strand	95-96	2	3
α-helix	99	1
β-strand	100-101	2	3
α-helix	102	1
α-helix	109-116	8
α-helix	121-123	3
α-helix	124-128	5
α-helix	137-145	9
α-helix	152-156	5
β-strand	160-164	5	3
α-helix	165-173	9
β-strand	180-182	3	4
α-helix	183-187	5
β-strand	192-193	2	5
β-strand	198-199	2	5
α-helix	201-203	3
α-helix	204-208	5
α-helix	214-215	2
β-strand	216-218	3	4
β-strand	226-228	3	6
β-strand	236-238	3	6
β-strand	239	1	1
β-strand	243-244	2	1
α-helix	245-252	8
β-strand	261-265	5	7
β-strand	269-276	8	7
β-strand	287-292	6	7
β-strand	298-306	9	7
α-helix	310-315	6
α-helix	316-320	5
α-helix	326-328	3
α-helix	329-335	7
β-strand	343-345	3	8
β-strand	348	1	9
β-strand	350	1	9
β-strand	352	1	7
β-strand	362-367	6	8
α-helix	373-395	23
α-helix	396-400	5
β-strand	405-409	5	7
α-helix	411-414	4
α-helix	416-426	11
β-strand	429-433	5	7
α-helix	438-449	12
α-helix	457-460	4
α-helix	461-463	3
β-strand	466-470	5	7
α-helix	476-491	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycerol kinase	O, Y	protein	501	Escherichia coli	P0A6F3 (AlphaFold model)

Sequence of entity 1 (O, Y), FASTA

>1BWF_1 GLYCEROL KINASE (chains O, Y)
TEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSWTL
VEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGL
EDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHV
TDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPIS
GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNY
ALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYA
RGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ
FQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERN
YRYAGWKKAVKRAMAWEEHDE

Ligands and cofactors

ID	Name	Formula	Copies
ATF	Phosphodifluoromethylphosphonic acid-adenylate ester	C11 H16 F2 N5 O12 P3	2
MG	Magnesium ion	Mg	2

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

Primary citation

Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion. Bystrom, C.E., Pettigrew, D.W., Branchaud, B.P. et al. Biochemistry (1999) 38:3508-3518. DOI 10.1021/bi982460z · PubMed

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

3EZW 2.0 Å, Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 -->…
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…
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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