2glj

crystal structure of aminopeptidase I from Clostridium acetobutylicum

Method: X-RAY DIFFRACTION

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

Probable M18-family aminopeptidase 1

Clostridium acetobutylicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	MANGANESE (II) ION × 24 water × 12	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	MANGANESE (II) ION × 24 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APEA_CLOAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–461； UniProt 5–465 Author chain B； PDBConstruct 1–461； UniProt 5–465 Author chain C； PDBConstruct 1–461； UniProt 5–465 Author chain D； PDBConstruct 1–461； UniProt 5–465 Author chain E； PDBConstruct 1–461； UniProt 5–465 Author chain F； PDBConstruct 1–461； UniProt 5–465 Author chain G； PDBConstruct 1–461； UniProt 5–465 Author chain H； PDBConstruct 1–461； UniProt 5–465 Author chain I； PDBConstruct 1–461； UniProt 5–465 Author chain J； PDBConstruct 1–461； UniProt 5–465 Author chain K； PDBConstruct 1–461； UniProt 5–465 Author chain L； PDBConstruct 1–461； UniProt 5–465 Author chain M； PDBConstruct 1–461； UniProt 5–465 Author chain N； PDBConstruct 1–461； UniProt 5–465 Author chain O； PDBConstruct 1–461； UniProt 5–465 Author chain P； PDBConstruct 1–461； UniProt 5–465 Author chain Q； PDBConstruct 1–461； UniProt 5–465 Author chain R； PDBConstruct 1–461； UniProt 5–465 Author chain S； PDBConstruct 1–461； UniProt 5–465 Author chain T； PDBConstruct 1–461； UniProt 5–465 Author chain U； PDBConstruct 1–461； UniProt 5–465 Author chain V； PDBConstruct 1–461； UniProt 5–465 Author chain W； PDBConstruct 1–461； UniProt 5–465 Author chain X； PDBConstruct 1–461； UniProt 5–465

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	2glj
Deposition date deposition_date	2006-04-04
Structure title title	crystal structure of aminopeptidase I from Clostridium acetobutylicum
Keywords keywords	;aminopeptidase I, NYSGXRC, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, 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.

2glj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2glj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2glj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	51.72 Å
Rg (electron density)	51.28 Å
Total Rg	51.62 Å
Atom count	42996
Residues	5460
Excluded volume	768850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2glj__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2glj__assembly_2__model_1`	dodecameric （12）	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 (3)

Entity 1 Entity 1 polymer

Description description	Probable M18-family aminopeptidase 1
Molecular weight formula_weight	51664.6 kDa
EC 编号 ec_number	3.4.11.-
Source method src_method	man
Copy count entity_count	24

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Atom count atom_count	91225

LLKEYKNAWDKYDDKQLKEVFALGDRFKNFISNCKTERECVTELIKTAEKSGYRNIEDILAKGETLKEGDKVYANNRGKGLIMFLIGKEPLYTGFKILGAHIDSPRLDLKQNPLYEDTDLAMLETHYYGGIKKYQWVTLPLAIHGVIVKKDGTIVNVCVGEDDNDPVFGVSDILVHLASEQLEKKASKVIEGEDLNILIGSIPLKDGEEKQKVKHNIMKILNEKYDISEEDFVSAELEIVPAGKARDYGFDRSMVMGYGQDDRICAYTSFEAMLEMKNAKKTCITILVDKEEVGSIGATGMQSKFFENTVADIMSLCGDYDELKLRKALYNSEMLSSDVSAAFDPNYPNVMEKRNSAYLGKGIVFNKYTGSRGKSGCNDANPEYIAELRRILSKESVNWQTAELGKVDQGGGGTIAYILAEYGMQVIDCGVALLNMHAPWEISSKADIYETKNGYSAFLNN

Source Source

Source organism organism	Clostridium acetobutylicum
NCBI taxonomy ID ncbi_taxonomy_id	1488
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	48

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5233

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6. Fold Classification (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

Domain ID domain_id	2gljA01
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	2gljA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljB01
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	2gljB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljC01
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	2gljC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljD01
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	2gljD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljE01
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	2gljE02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljF01
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	2gljF02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljG01
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	2gljG02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljH01
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	2gljH02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljI01
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	2gljI02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljJ01
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	2gljJ02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljK01
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	2gljK02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljL01
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	2gljL02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljM01
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	2gljM02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljN01
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	2gljN02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljO01
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	2gljO02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljP01
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	2gljP02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljQ01
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	2gljQ02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljR01
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	2gljR02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljS01
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	2gljS02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljT01
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	2gljT02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljU01
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	2gljU02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljV01
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	2gljV02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljW01
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	2gljW02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

Domain ID domain_id	2gljX01
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	2gljX02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	250 — Aminopeptidase i, Domain 2
Homologous superfamily homologous superfamily	10 — Aminopeptidase i, Domain 2

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Unit-cell length a length_a	121.708 Å
Unit-cell length b length_b	129.680 Å
Unit-cell length c length_c	222.728 Å
Unit-cell angle α angle_alpha	89.88 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	116.68 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2500
R_work r_work	0.2500
R_free r_free	0.2970

crystal structure of aminopeptidase I from Clostridium acetobutylicum

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

Probable M18-family aminopeptidase 1

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

2glj__assembly_2__model_1

2glj__assembly_2__model_1 | I(q)

2glj__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

7. Citations (1)

crystal structure of aminopeptidase I from Clostridium acetobutylicum

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

Probable M18-family aminopeptidase 1

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

2glj__assembly_2__model_1

2glj__assembly_2__model_1 | I(q)

2glj__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 48 domains

CATH v4.4 (48 domains)

7. Citations (1)