3BDF: Metal-free E. coli alkaline phosphatase

Crystal structure of metal-free E. coli alkaline phosphatase (T155V). Determined by X-ray diffraction at 1.4 Å resolution. Released 25 Nov 2008.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Escherichia coli
Chains: 2
Atoms: 7,819
Mol. weight: 97.03 kDa
Released: 25 Nov 2008

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

Secondary structure: helices and β-sheets

3BDF contains 45 α-helices and 56 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: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
α-helix	30-34	5
α-helix	41-42	2
β-strand	44-50	7	1
α-helix	55-66	12
α-helix	75-77	3
β-strand	80-85	6	1
β-strand	88-89	2	2
β-strand	96-97	2	2
α-helix	102-111	10
β-strand	116	1	2
β-strand	120	1	3
β-strand	122	1	4
β-strand	128	1	4
α-helix	132-138	7
β-strand	142-150	9	1
α-helix	154-158	5
β-strand	163	1	3
α-helix	171-177	7
α-helix	179-181	3
α-helix	183-185	3
α-helix	191-198	8
β-strand	202-206	5	1
α-helix	208-212	5
β-strand	214	1	5
β-strand	215	1	6
β-strand	221	1	6
β-strand	224	1	5
α-helix	225-231	7
β-strand	235-237	3	1
α-helix	240-244	5
β-strand	255-258	4	1
α-helix	264-266	3
β-strand	268-269	2	7
α-helix	271-273	3
β-strand	274-275	2	8
α-helix	277-280	4
α-helix	282-283	2
β-strand	284	1	8
β-strand	287-288	2	7
α-helix	299-310	12
β-strand	317-323	7	1
α-helix	335-359	25
β-strand	362-368	7	1
β-strand	374-377	4	8
β-strand	386-391	6	8
β-strand	397-402	6	8
β-strand	417-422	6	1
α-helix	426-429	4
β-strand	431-434	4	1
α-helix	435-445	11

Chain B: 22 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	30-35	6
α-helix	41-42	2
β-strand	44-50	7	1
α-helix	55-66	12
α-helix	75-77	3
β-strand	80-85	6	1
β-strand	88-89	2	9
β-strand	96-97	2	9
α-helix	102-111	10
β-strand	116	1	9
β-strand	120	1	10
β-strand	122	1	11
β-strand	128	1	11
α-helix	132-138	7
β-strand	142-150	9	1
α-helix	154-158	5
β-strand	163	1	10
α-helix	171-177	7
α-helix	179-181	3
α-helix	183-185	3
α-helix	191-198	8
β-strand	202-206	5	1
α-helix	209-212	4
β-strand	214	1	12
β-strand	215	1	13
β-strand	221	1	13
β-strand	224	1	12
α-helix	225-231	7
β-strand	235-237	3	1
α-helix	240-244	5
β-strand	255-258	4	1
α-helix	264-266	3
β-strand	268-269	2	14
α-helix	271-273	3
β-strand	274	1	15
α-helix	277-280	4
α-helix	282-283	2
β-strand	284	1	15
β-strand	287-288	2	14
α-helix	299-310	12
β-strand	317-323	7	1
α-helix	335-359	25
β-strand	362-368	7	1
β-strand	375-377	3	15
β-strand	386-391	6	15
β-strand	397-402	6	15
β-strand	417-422	6	1
α-helix	426-429	4
β-strand	431-434	4	1
α-helix	435-446	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alkaline phosphatase	A, B	protein	458	Escherichia coli	P00634 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3BDF_1 Alkaline phosphatase (chains A, B)
RTPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEIT
AARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGA
LGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDAVPAALVAHVTSRKCYGPSATSEKCP
GNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSD
AASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTL
AQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKE
GNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRI
AAYGPHAANVVGLTDQTDLFYTMKAALGLKLEHHHHHH

Primary citation

The Active-Site Trimetallic Cluster of Alkaline Phosphatase is Lost Upon Isosteric Mutation at the Mg2+-Coordinating Residue Threonine-155. Grigg, J.C., Hucaluk, C., Murphy, M.E. et al. To be published.

Other PDB entries of the same protein (UniProt P00634 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TG0 1.2 Å, E. coli alkaline phosphatase with bound inorganic phosphate
3BDG 1.4 Å, Crystal structure of wild-type/T155V mixed dimer of E. coli alkaline phosphatase
1Y6V 1.6 Å, Structure of E. coli Alkaline Phosphatase in presence of cobalt at 1.60 A resolution
1ED8 1.75 Å, Structure of E. Coli alkaline phosphatase inhibited by the inorganic phosphate at 1.75A…
1ED9 1.75 Å, Structure of E. Coli alkaline phosphatase without the inorganic phosphate at 1.75A…
1Y7A 1.77 Å, Structure of D153H/K328W E. coli alkaline phosphatase in presence of cobalt at 1.77 A…
7N6M 1.82 Å, Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the…
3BDH 1.85 Å, Crystal structure of zinc-deficient wild-type E. coli alkaline phosphatase
1B8J 1.9 Å, Alkaline phosphatase complexed with vanadate
1ALK 2.0 Å, Reaction mechanism of alkaline phosphatase based on crystal structures. Two metal ion…
1EW9 2.0 Å, Alkaline phosphatase (e.c. 3.1.3.1) complex with mercaptomethyl phosphonate
1KH5 2.0 Å, E. Coli alkaline phosphatase mutant (D330N) mimic of the transition states with…

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