1sql

Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine

Method: X-RAY DIFFRACTION

▼

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

dihydroneopterin aldolase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	GUANINE × 8 water × 8	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	GUANINE × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9SF23_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 1–146 Author chain B； PDBConstruct 1–146； UniProt 1–146 Author chain C； PDBConstruct 1–146； UniProt 1–146 Author chain D； PDBConstruct 1–146； UniProt 1–146 Author chain E； PDBConstruct 1–146； UniProt 1–146 Author chain F； PDBConstruct 1–146； UniProt 1–146 Author chain G； PDBConstruct 1–146； UniProt 1–146 Author chain H； PDBConstruct 1–146； UniProt 1–146 Author chain I； PDBConstruct 1–146； UniProt 1–146 Author chain J； PDBConstruct 1–146； UniProt 1–146 Author chain K； PDBConstruct 1–146； UniProt 1–146 Author chain L； PDBConstruct 1–146； UniProt 1–146 Author chain M； PDBConstruct 1–146； UniProt 1–146 Author chain N； PDBConstruct 1–146； UniProt 1–146 Author chain O； PDBConstruct 1–146； UniProt 1–146 Author chain P； PDBConstruct 1–146； UniProt 1–146

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	1sql
Deposition date deposition_date	2004-03-19
Structure title title	Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine
Keywords keywords	tetrahydrofolate biosynthesis, aldolase classes, retroaldol reaction, purin binding, Schiff base, LYASE; 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.

1sql__assembly_1__model_1

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

Download this curve (.dat)

1sql__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1sql__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.35 Å
Rg (electron density)	28.64 Å
Total Rg	29.56 Å
Atom count	7718
Residues	967
Excluded volume	139050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1sql__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1sql__assembly_2__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

▼

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1sqla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqld_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqle_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqli_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqll_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqln_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlo_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

Domain ID domain_id	d1sqlp_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

CATH v4.4 (16 domains)

Domain ID domain_id	1sqlA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlN00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1sqlP00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

▶

Unit-cell length a length_a	63.550 Å
Unit-cell length b length_b	84.220 Å
Unit-cell length c length_c	89.050 Å
Unit-cell angle α angle_alpha	90.14 °
Unit-cell angle β angle_beta	89.99 °
Unit-cell angle γ angle_gamma	76.17 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2040
R_free r_free	0.2600

Description description	dihydroneopterin aldolase
Molecular weight formula_weight	16302.6 kDa
Source method src_method	nat
Copy count entity_count	16

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
Atom count atom_count	16400

Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine

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

dihydroneopterin aldolase

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

1sql__assembly_1__model_1

1sql__assembly_1__model_1 | I(q)

1sql__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Description description	GUANINE
Molecular weight formula_weight	151.1 kDa
Source method src_method	syn
Copy count entity_count	16

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	929

Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine

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

dihydroneopterin aldolase

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

1sql__assembly_1__model_1

1sql__assembly_1__model_1 | I(q)

1sql__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)