1gyt

E. coli Aminopeptidase A (PepA)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOSOL AMINOPEPTIDASE

ESCHERICHIA COLI K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 12 CARBONATE ION × 6 CHLORIDE ION × 2 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 12 CARBONATE ION × 6 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–503； UniProt 1–503 Author chain B； PDBConstruct 1–503； UniProt 1–503 Author chain C； PDBConstruct 1–503； UniProt 1–503 Author chain D； PDBConstruct 1–503； UniProt 1–503 Author chain E； PDBConstruct 1–503； UniProt 1–503 Author chain F； PDBConstruct 1–503； UniProt 1–503 Author chain G； PDBConstruct 1–503； UniProt 1–503 Author chain H； PDBConstruct 1–503； UniProt 1–503 Author chain I； PDBConstruct 1–503； UniProt 1–503 Author chain J； PDBConstruct 1–503； UniProt 1–503 Author chain K； PDBConstruct 1–503； UniProt 1–503 Author chain L； PDBConstruct 1–503； UniProt 1–503

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gyt
Deposition date deposition_date	2002-04-29
Structure title title	E. coli Aminopeptidase A (PepA)
Keywords keywords	HYDROLASE, PEPTIDASE, DNA RECOMBINATION, AMINOPEPTIDASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1gyt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1gyt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1gyt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	44.63 Å
Rg (electron density)	44.32 Å
Total Rg	44.50 Å
Atom count	23114
Residues	3018
Excluded volume	410520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1gyt__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1gyt__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CYTOSOL AMINOPEPTIDASE
Molecular weight formula_weight	54945.7 kDa
EC 编号 ec_number	3.4.11.1
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	49952

MEFSVKSGSPEKQRSACIVVGVFEPRRLSPIAEQLDKISDGYISALLRRGELEGKPGQTLLLHHVPNVLSERILLIGCGKERELDERQYKQVIQKTINTLNDTGSMEAVCFLTELHVKGRNNYWKVRQAVETAKETLYSFDQLKTNKSEPRRPLRKMVFNVPTRRELTSGERAIQHGLAIAAGIKAAKDLGNMPPNICNAAYLASQARQLADSYSKNVITRVIGEQQMKELGMHSYLAVGQGSQNESLMSVIEYKGNASEDARPIVLVGKGLTFDSGGISIKPSEGMDEMKYDMCGAAAVYGVMRMVAELQLPINVIGVLAGCENMPGGRAYRPGDVLTTMSGQTVEVLNTDAEGRLVLCDVLTYVERFEPEAVIDVATLTGACVIALGHHITGLMANHNPLAHELIAASEQSGDRAWRLPLGDEYQEQLESNFADMANIGGRPGGAITAGCFLSRFTRKYNWAHLDIAGTAWRSGKAKGATGRPVALLAQFLLNRAGFNGEE

Source Source

Source organism organism	ESCHERICHIA COLI K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI K-12

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3724

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1gyta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gyta2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gyte1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gyte2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytg1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gyth1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gyth2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gyti1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gyti2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytj1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytj2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytk1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytk2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

Domain ID domain_id	d1gytl1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

Domain ID domain_id	d1gytl2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.3 — Leucine aminopeptidase, C-terminal domain

CATH v4.4 (24 domains)

Domain ID domain_id	1gytA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytJ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytK02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1gytL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	1gytL02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

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Unit-cell length a length_a	178.000 Å
Unit-cell length b length_b	178.000 Å
Unit-cell length c length_c	244.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1650
R_work r_work	0.1650
R_free r_free	0.2090

E. coli Aminopeptidase A (PepA)

1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOSOL AMINOPEPTIDASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1gyt__assembly_1__model_1

1gyt__assembly_1__model_1 | I(q)

1gyt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)

E. coli Aminopeptidase A (PepA)

1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOSOL AMINOPEPTIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1gyt__assembly_1__model_1

1gyt__assembly_1__model_1 | I(q)

1gyt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)