1ED9: Alkaline phosphatase

Structure of E. Coli alkaline phosphatase without the inorganic phosphate at 1.75A resolution. Determined by X-ray diffraction at 1.75 Å resolution. Released 20 Sept 2000.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Escherichia coli
Chains: 2
Atoms: 7,240
Mol. weight: 94.69 kDa
Ligands: MG, ZN
Released: 20 Sept 2000

Explore 1ED9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ED9 contains 49 α-helices and 58 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: 26 helices, 30 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	55-65	11
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	154-157	4
β-strand	163	1	3
α-helix	171-177	7
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
α-helix	234	1
β-strand	235-237	3	1
α-helix	240-245	6
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	290-292	3
α-helix	297-298	2
α-helix	299-310	12
β-strand	317-323	7	1
α-helix	325-331	7
α-helix	335-359	25
β-strand	362-368	7	1
β-strand	371	1	9
β-strand	375-377	3	8
β-strand	386-391	6	8
β-strand	397-402	6	8
α-helix	410-412	3
β-strand	413	1	9
β-strand	417-422	6	1
α-helix	426-429	4
β-strand	431-434	4	1
α-helix	435-446	12

Chain B: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	530-534	5
α-helix	541-542	2
β-strand	544-550	7	10
α-helix	555-565	11
α-helix	575-577	3
β-strand	580-585	6	10
β-strand	588-589	2	11
β-strand	596-597	2	11
α-helix	602-611	10
β-strand	616	1	11
β-strand	620	1	12
β-strand	622	1	13
β-strand	628	1	13
α-helix	632-638	7
β-strand	642-650	9	10
α-helix	654-657	4
β-strand	663	1	12
α-helix	671-677	7
α-helix	679-681	3
α-helix	691-698	8
β-strand	702-706	5	10
α-helix	709-712	4
β-strand	714	1	14
β-strand	724	1	14
α-helix	725-731	7
β-strand	735-737	3	10
α-helix	740-745	6
β-strand	755-758	4	10
α-helix	764-766	3
β-strand	768-769	2	15
α-helix	771-773	3
β-strand	774	1	16
α-helix	777-780	4
α-helix	782-783	2
β-strand	784	1	16
β-strand	787-788	2	15
α-helix	799-810	12
β-strand	817-823	7	10
α-helix	825-831	7
α-helix	835-859	25
β-strand	862-868	7	10
β-strand	871	1	17
β-strand	875-877	3	16
β-strand	886-891	6	16
β-strand	897-902	6	16
α-helix	910-912	3
β-strand	913	1	17
β-strand	917-922	6	10
α-helix	926-929	4
β-strand	931-934	4	10
α-helix	935-946	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alkaline phosphatase	A, B	protein	449	Escherichia coli	P00634 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1ED9_1 ALKALINE PHOSPHATASE (chains A, B)
TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITA
ARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGAL
GVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPG
NALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDA
ASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLA
QMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEG
NTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIA
AYGPHAANVVGLTDQTDLFYTMKAALGLK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

A revised mechanism for the alkaline phosphatase reaction involving three metal ions. Stec, B., Holtz, K.M., Kantrowitz, E.R. J Mol Biol (2000) 299:1303-1311. DOI 10.1006/jmbi.2000.3799 · PubMed

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
3BDF 1.4 Å, Crystal structure of metal-free E. coli alkaline phosphatase (T155V)
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…
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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