2zc0

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

Method: X-RAY DIFFRACTION

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

Alanine glyoxylate transaminase

Thermococcus litoralis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 4 IMIDAZOLE × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2 IMIDAZOLE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2 IMIDAZOLE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9C4M4_THELI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–407； UniProt 1–407 Author chain B； PDBConstruct 1–407； UniProt 1–407 Author chain C； PDBConstruct 1–407； UniProt 1–407 Author chain D； PDBConstruct 1–407； UniProt 1–407

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	2zc0
Deposition date deposition_date	2007-10-31
Structure title title	Crystal structure of an archaeal alanine:glyoxylate aminotransferase
Keywords keywords	alanine:glyoxylate aminotransferase, archaea, Thermococcus litoralis, 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.

2zc0__assembly_1__model_1

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

Download this curve (.dat)

2zc0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zc0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.07 Å
Rg (electron density)	35.39 Å
Total Rg	35.80 Å
Atom count	12532
Residues	1620
Excluded volume	226510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zc0__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zc0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zc0__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Alanine glyoxylate transaminase
Molecular weight formula_weight	45227.7 kDa
EC 编号 ec_number	2.6.1.44
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12914

MDYTKYLAGRANWIKGSALADVMKKASELQKKGVKLISLAAGDPDPELIPRAVLGEIAKEVLEKEPKSVMYTPANGIPELREELAAFLKKYDHLEVSPENIVITIGGTGALDLLGRVLIDPGDVVITENPSYINTLLAFEQLGAKIEGVPVDNDGMRVDLLEEKIKELKAKGQKVKLIYTIPTGQNPMGVTMSMERRKALLEIASKYDLLIIEDTAYNFMRYEGGDIVPLKALDNEGRVIVAGTLSKVLGTGFRIGWIIAEGEILKKVLMQKQPIDFCAPAISQYIALEYLKRGYFEKYHLEGALLGYKEKRDIMLKALENHLPNAEFTKPIAGMFVMFFLPEGADGISFANELMEREGVVVVPGKPFYTDESGKNAIRLNFSRPSKEEIPIGIKKLAKLYKEKFGE

Source Source

Source organism organism	Thermococcus litoralis
NCBI taxonomy ID ncbi_taxonomy_id	2265
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	248.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	382

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2zc0a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.0 — automated matches

Domain ID domain_id	d2zc0b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.0 — automated matches

Domain ID domain_id	d2zc0c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.0 — automated matches

Domain ID domain_id	d2zc0d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2zc0A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zc0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2zc0B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zc0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2zc0C01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zc0C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2zc0D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zc0D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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Unit-cell length a length_a	77.694 Å
Unit-cell length b length_b	112.519 Å
Unit-cell length c length_c	207.287 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	49.400 Å
R factor r_factor	—
R_work r_work	0.2360
R_free r_free	0.2610

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

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

Alanine glyoxylate transaminase

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

2zc0__assembly_1__model_1

2zc0__assembly_1__model_1 | I(q)

2zc0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of an archaeal alanine:glyoxylate aminotransferase

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

Alanine glyoxylate transaminase

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

2zc0__assembly_1__model_1

2zc0__assembly_1__model_1 | I(q)

2zc0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)