SAXSdb — 1k9x

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

M32 carboxypeptidase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U3L0_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–499； UniProt 1–499 Author chain B； PDBConstruct 1–499； UniProt 1–499 Author chain C； PDBConstruct 1–499； UniProt 1–499 Author chain D； PDBConstruct 1–499； UniProt 1–499

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	1k9x
Deposition date deposition_date	2001-10-31
Structure title title	Structure of Pyrococcus furiosus carboxypeptidase Apo-Yb
Keywords keywords	HEXXH motif, M32 family, metallopeptidase, carboxypeptidase; carboxypeptidase
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.

1k9x__assembly_1__model_1

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

Download this curve (.dat)

1k9x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k9x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.63 Å
Rg (electron density)	33.07 Å
Total Rg	33.79 Å
Atom count	8326
Residues	994
Excluded volume	149210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k9x__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k9x__assembly_2__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1k9xa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

Domain ID domain_id	d1k9xb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

Domain ID domain_id	d1k9xc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

Domain ID domain_id	d1k9xd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.5 — Neurolysin-like

CATH v4.4 (4 domains)

Domain ID domain_id	1k9xA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1k9xB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1k9xC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1k9xD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	66.342 Å
Unit-cell length b length_b	86.780 Å
Unit-cell length c length_c	107.895 Å
Unit-cell angle α angle_alpha	88.64 °
Unit-cell angle β angle_beta	78.54 °
Unit-cell angle γ angle_gamma	69.44 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.780 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2670

Description description	M32 carboxypeptidase
Molecular weight formula_weight	59127.7 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17261

Structure of Pyrococcus furiosus carboxypeptidase Apo-Yb

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

M32 carboxypeptidase

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

1k9x__assembly_1__model_1

1k9x__assembly_1__model_1 | I(q)

1k9x__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	609

Structure of Pyrococcus furiosus carboxypeptidase Apo-Yb

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

M32 carboxypeptidase

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

1k9x__assembly_1__model_1

1k9x__assembly_1__model_1 | I(q)

1k9x__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)