2yce

Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.

Method: X-RAY DIFFRACTION

▼

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

FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1

THERMOPROTEUS TENAX

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	D-MANNITOL-1,6-DIPHOSPHATE × 5 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	D-MANNITOL-1,6-DIPHOSPHATE × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALF1_THETE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 1–263 Author chain B； PDBConstruct 1–263； UniProt 1–263 Author chain C； PDBConstruct 1–263； UniProt 1–263 Author chain D； PDBConstruct 1–263； UniProt 1–263 Author chain E； PDBConstruct 1–263； UniProt 1–263 Author chain F； PDBConstruct 1–263； UniProt 1–263 Author chain G； PDBConstruct 1–263； UniProt 1–263 Author chain H； PDBConstruct 1–263； UniProt 1–263 Author chain I； PDBConstruct 1–263； UniProt 1–263 Author chain J； PDBConstruct 1–263； UniProt 1–263

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2yce
Deposition date deposition_date	2011-03-14
Structure title title	Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.
Keywords keywords	LYASE, GLYCOLYSIS; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2yce__assembly_1__model_1

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

Download this curve (.dat)

2yce__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yce__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.53 Å
Rg (electron density)	33.75 Å
Total Rg	34.35 Å
Atom count	9806
Residues	1256
Excluded volume	175750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yce__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yce__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
Molecular weight formula_weight	28741.1 kDa
EC 编号 ec_number	4.1.2.13
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	21227

MANLTEKFLRIFARRGKSIILAYDHGIEHGPADFMDNPDSADPEYILRLARDAGFDGVVFQRGIAEKYYDGSVPLILKLNGKTTLYNGEPVSVANCSVEEAVSLGASAVGYTIYPGSGFEWKMFEELARIKRDAVKFDLPLVVWSFPRGGKVVNETAPEIVAYAARIALELGSDAMKIKYTGDPKTFSWAVKVAGKVPVLMSGGPKTKTEEDFLKQVEGVLEAGALGIAVGRNVWQRRDALKFARALAELVYGGKKLAEPLNV

Source Source

Source organism organism	THERMOPROTEUS TENAX
NCBI taxonomy ID ncbi_taxonomy_id	2271
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	D-MANNITOL-1,6-DIPHOSPHATE
Molecular weight formula_weight	342.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1518

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2ycea1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2yceb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2ycec_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2yced_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2ycee_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2ycef_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2yceg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2yceh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2ycei_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d2ycej_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

CATH v4.4 (10 domains)

Domain ID domain_id	2yceA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceE00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceF00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceG00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceH00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceI00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	2yceJ00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

▶

Unit-cell length a length_a	82.900 Å
Unit-cell length b length_b	159.200 Å
Unit-cell length c length_c	101.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	39.800 Å
R factor r_factor	0.1565
R_work r_work	0.1559
R_free r_free	0.1981

Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.

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

FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 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

2yce__assembly_1__model_1

2yce__assembly_1__model_1 | I(q)

2yce__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 (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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.

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

FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 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

2yce__assembly_1__model_1

2yce__assembly_1__model_1 | I(q)

2yce__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 (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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)