4u0z

Eukaryotic Fic Domain containing protein with bound APCPP

Method: X-RAY DIFFRACTION

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

Adenosine monophosphate-protein transferase FICD

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FICD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–344； UniProt 102–445 Author chain B； PDBConstruct 1–344； UniProt 102–445 Author chain C； PDBConstruct 1–344； UniProt 102–445 Author chain D； PDBConstruct 1–344； UniProt 102–445 Author chain E； PDBConstruct 1–344； UniProt 102–445 Author chain F； PDBConstruct 1–344； UniProt 102–445 Author chain G； PDBConstruct 1–344； UniProt 102–445 Author chain H； PDBConstruct 1–344； UniProt 102–445

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	4u0z
Deposition date deposition_date	2014-07-14
Structure title title	Eukaryotic Fic Domain containing protein with bound APCPP
Keywords keywords	TPR, FIC, APCPP, adenylation, transferase; TRANSFERASE
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.

4u0z__assembly_1__model_1

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

Download this curve (.dat)

4u0z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4u0z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.01 Å
Rg (electron density)	34.43 Å
Total Rg	34.58 Å
Atom count	5114
Residues	644
Excluded volume	90710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4u0z__assembly_1__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4u0z__assembly_2__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4u0z__assembly_3__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4u0z__assembly_4__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4u0z__assembly_5__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4u0z__assembly_6__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4u0z__assembly_7__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 (4)

Entity 1 Entity 1 polymer

Description description	Adenosine monophosphate-protein transferase FICD
Molecular weight formula_weight	39548.3 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	21328

GKLEARAALNQALEMKRQGKREKAQKLFMHALKMDPDFVDALTEFGIFSEEDKDIIQADYLYTRALTISPYHEKALVNRDRTLPLVEEIDQRYFSIIDSKVKKVMSIPKGNSALRRVMEETYYHHIYHTVAIEGNTLTLSEIRHILETRYAVPGKSLEEQNEVIGMHAAMKYINTTLVSRIGSVTISDVLEIHRRVLGYVDPVEAGRFRTTQVLVGHHIPPHPQDVEKQMQEFVQWLNSEEAMNLHPVEFAALAHYKLVYIHPFIDGNGRTSRLLMNLILMQAGYPPITIRKEQRSDYYHVLEAANEGDVRPFIRFIAKCTETTLDTLLFATTEYSVALPEAQP

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	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	816

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	4u0zA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zB01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zD01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zE01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zF01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zG01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	4u0zH01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4u0zH02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

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Unit-cell length a length_a	77.100 Å
Unit-cell length b length_b	83.754 Å
Unit-cell length c length_c	130.023 Å
Unit-cell angle α angle_alpha	89.92 °
Unit-cell angle β angle_beta	89.57 °
Unit-cell angle γ angle_gamma	89.43 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	43.340 Å
R factor r_factor	0.2082
R_work r_work	0.2059
R_free r_free	0.2511

Eukaryotic Fic Domain containing protein with bound APCPP

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

Adenosine monophosphate-protein transferase FICD

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

4u0z__assembly_1__model_1

4u0z__assembly_1__model_1 | I(q)

4u0z__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 (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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Eukaryotic Fic Domain containing protein with bound APCPP

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

Adenosine monophosphate-protein transferase FICD

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

4u0z__assembly_1__model_1

4u0z__assembly_1__model_1 | I(q)

4u0z__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 (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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)