2c4k

Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)

Method: X-RAY DIFFRACTION

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

PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 TRIS(HYDROXYETHYL)AMINOMETHANE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPRA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–370； UniProt 5–351 Author chain B； PDBConstruct 24–370； UniProt 5–351 Author chain C； PDBConstruct 24–370； UniProt 5–351 Author chain D； PDBConstruct 24–370； UniProt 5–351 Author chain E； PDBConstruct 24–370； UniProt 5–351 Author chain F； PDBConstruct 24–370； UniProt 5–351

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	2c4k
Deposition date deposition_date	2005-10-20
Structure title title	Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)
Keywords keywords	NUCLEOTIDE BIOSYNTHESIS, SYNTHETASE, LIGASE, REGULATORY PROTEIN; REGULATORY PROTEIN
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.

2c4k__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2c4k__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c4k__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	21.44 Å
Rg (electron density)	20.19 Å
Total Rg	21.09 Å
Atom count	2386
Residues	305
Excluded volume	42970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c4k__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2c4k__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2c4k__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2c4k__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2c4k__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2c4k__assembly_6__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1
Molecular weight formula_weight	41202.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14378

MHHHHHHSSGVDLGTENLYFQSMRTGYRVFSANSTAACTELAKRITERLGAELGKSVVYQETNGETRVEIKESVRGQDIFIIQTIPRDVNTAVMELLIMAYALKTACARNIIGVIPYFPYSKQSKMRKRGSIVCKLLASMLAKAGLTHIITMDLHQKEIQGFFSFPVDNLRASPFLLQYIQEEIPNYRNAVIVAKSPDAAKRAQSYAERLRLGLAVIHGEAQCTELDMDDGRHSPPMVKNATVHPGLELPLMMAKEKPPITVVGDVGGRIAIIVDDIIDDVESFVAAAEILKERGAYKIYVMATHGILSAEAPRLIEESSVDEVVVTNTVPHEVQKLQCPKIKTVDISLILSEAIRRIHNGESMAYLFRN

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2c4ka1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4ka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4ke1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4ke2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

Domain ID domain_id	d2c4kf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.2 — Phosphoribosylpyrophosphate synthetase-like

CATH v4.4 (12 domains)

Domain ID domain_id	2c4kA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	2c4kF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

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Unit-cell length a length_a	180.055 Å
Unit-cell length b length_b	103.875 Å
Unit-cell length c length_c	127.161 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2710
R_work r_work	0.2690
R_free r_free	0.2990

Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)

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

PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 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

2c4k__assembly_5__model_1

2c4k__assembly_5__model_1 | I(q)

2c4k__assembly_5__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)

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

PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 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

2c4k__assembly_5__model_1

2c4k__assembly_5__model_1 | I(q)

2c4k__assembly_5__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)