1w7v

ZnMg substituted aminopeptidase P from E. coli

Method: X-RAY DIFFRACTION

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

XAA-PRO AMINOPEPTIDASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	PEPTIDE VAL-PRO-LEU × 4 ZINC ION × 4 MAGNESIUM ION × 6 CHLORIDE ION × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	PEPTIDE VAL-PRO-LEU × 4 ZINC ION × 4 MAGNESIUM ION × 6 CHLORIDE ION × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMPP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–440； UniProt 1–440 Author chain B； PDBConstruct 1–440； UniProt 1–440 Author chain C； PDBConstruct 1–440； UniProt 1–440 Author chain D； PDBConstruct 1–440； UniProt 1–440

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	1w7v
Deposition date deposition_date	2004-09-13
Structure title title	ZnMg substituted aminopeptidase P from E. coli
Keywords keywords	HYDROLASE, PROLINE-SPECIFIC PEPTIDASE, METALLOENZYME, PITA-BREAD FOLD, DINUCLEAR HYDROLASE; 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.

1w7v__assembly_1__model_1

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

Download this curve (.dat)

1w7v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w7v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.71 Å
Rg (electron density)	40.28 Å
Total Rg	40.82 Å
Atom count	14046
Residues	1762
Excluded volume	248320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w7v__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1w7v__assembly_2__model_1`	octameric （8）	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 (6)

Entity 1 Entity 1 polymer

Description description	XAA-PRO AMINOPEPTIDASE
Molecular weight formula_weight	49792.1 kDa
EC 编号 ec_number	3.4.11.9
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15192

SEISRQEFQRRRQALVEQMQPGSAALIFAAPEVTRSADSEYPYRQNSDFWYFTGFNEPEAVLVLIKSDDTHNHSVLFNRVRDLTAEIWFGRRLGQDAAPEKLGVDRALAFSEINQQLYQLLNGLDVVYHAQGEYAYADVIVNSALEKLRKGSRQNLTAPATMIDWRPVVHEMRLFKSPEEIAVLRRAGEITAMAHTRAMEKCRPGMFEYHLEGEIHHEFNRHGARYPSYNTIVGSGENGCILHYTENECEMRDGDLVLIDAGCEYKGYAGDITRTFPVNGKFTQAQREIYDIVLESLETSLRLYRPGTSILEVTGEVVRIMVSGLVKLGILKGDVDELIAQNAHRPFFMHGLSHWLGLDVHDVGVYGQDRSRILEPGMVLTVEPGLYIAPDAEVPEQYRGIGIRIEDDIVITETGNENLTASVVKKPEEIEALMVAARKQ

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PEPTIDE VAL-PRO-LEU
Molecular weight formula_weight	327.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

VPL

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1094

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1w7va1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1w7va2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

Domain ID domain_id	d1w7vb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1w7vb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

Domain ID domain_id	d1w7vc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1w7vc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

Domain ID domain_id	d1w7vd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1w7vd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (8 domains)

Domain ID domain_id	1w7vA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1w7vA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	1w7vB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1w7vB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	1w7vC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1w7vC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	1w7vD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1w7vD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

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Unit-cell length a length_a	111.731 Å
Unit-cell length b length_b	236.527 Å
Unit-cell length c length_c	137.997 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	37.800 Å
R factor r_factor	0.1570
R_work r_work	0.1560
R_free r_free	0.1800

ZnMg substituted aminopeptidase P from E. coli

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

XAA-PRO 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

1w7v__assembly_1__model_1

1w7v__assembly_1__model_1 | I(q)

1w7v__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

ZnMg substituted aminopeptidase P from E. coli

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

XAA-PRO 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

1w7v__assembly_1__model_1

1w7v__assembly_1__model_1 | I(q)

1w7v__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)