3a8i

Crystal Structure of ET-EHred-5-CH3-THF complex

Method: X-RAY DIFFRACTION

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

Aminomethyltransferase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Glycine cleavage system H protein × 1 （P0A6T9） 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Glycine cleavage system H protein × 1 （P0A6T9） 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCST_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–364； UniProt 1–364 Author chain B； PDBConstruct 1–364； UniProt 1–364 Author chain C； PDBConstruct 1–364； UniProt 1–364 Author chain D； PDBConstruct 1–364； UniProt 1–364

Glycine cleavage system H protein

Escherichia coli

UniProt P0A6T9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Aminomethyltransferase × 1 （P27248） 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Aminomethyltransferase × 1 （P27248） 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCSH_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–129； UniProt 1–129 Author chain F； PDBConstruct 1–129； UniProt 1–129

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	3a8i
Deposition date deposition_date	2009-10-06
Structure title title	Crystal Structure of ET-EHred-5-CH3-THF complex
Keywords keywords	Glycine Cleavage System, Aminotransferase, Transferase, Lipoyl, TRANSFERASE-TRANSPORT PROTEIN COMPLEX; TRANSFERASE/TRANSPORT 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.

3a8i__assembly_1__model_1

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

Download this curve (.dat)

3a8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a8i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.42 Å
Rg (electron density)	25.69 Å
Total Rg	26.27 Å
Atom count	3822
Residues	490
Excluded volume	67635 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a8i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3a8i__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3a8i__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3a8i__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Aminomethyltransferase
Molecular weight formula_weight	40190.6 kDa
EC 编号 ec_number	2.1.2.10
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	14524

MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEKGVLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRNGKAVA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Glycine cleavage system H protein
Molecular weight formula_weight	14009.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MSNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
Molecular weight formula_weight	459.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1124

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3a8ia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

Domain ID domain_id	d3a8ia2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.0 — automated matches

Domain ID domain_id	d3a8ib1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

Domain ID domain_id	d3a8ib2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.0 — automated matches

Domain ID domain_id	d3a8ic1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

Domain ID domain_id	d3a8ic2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.0 — automated matches

Domain ID domain_id	d3a8id1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

Domain ID domain_id	d3a8id2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.0 — automated matches

Domain ID domain_id	d3a8ie_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.1 — Single hybrid motif
Family Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

Domain ID domain_id	d3a8if_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.1 — Single hybrid motif
Family Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (18 domains)

Domain ID domain_id	3a8iA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	3a8iA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iA03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1250 — Aminomethyltransferase fragment
Homologous superfamily homologous superfamily	10 — Aminomethyltransferase fragment

Domain ID domain_id	3a8iA04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	3a8iB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iB03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1250 — Aminomethyltransferase fragment
Homologous superfamily homologous superfamily	10 — Aminomethyltransferase fragment

Domain ID domain_id	3a8iB04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	3a8iC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iC03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1250 — Aminomethyltransferase fragment
Homologous superfamily homologous superfamily	10 — Aminomethyltransferase fragment

Domain ID domain_id	3a8iC04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	3a8iD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iD03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1250 — Aminomethyltransferase fragment
Homologous superfamily homologous superfamily	10 — Aminomethyltransferase fragment

Domain ID domain_id	3a8iD04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	3a8iE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	3a8iF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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Unit-cell length a length_a	53.985 Å
Unit-cell length b length_b	88.928 Å
Unit-cell length c length_c	97.993 Å
Unit-cell angle α angle_alpha	91.53 °
Unit-cell angle β angle_beta	102.47 °
Unit-cell angle γ angle_gamma	89.59 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	29.770 Å
R factor r_factor	0.1851
R_work r_work	0.1820
R_free r_free	0.2443

Crystal Structure of ET-EHred-5-CH3-THF complex

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

Aminomethyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Glycine cleavage system H protein

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

3a8i__assembly_1__model_1

3a8i__assembly_1__model_1 | I(q)

3a8i__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (10 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Crystal Structure of ET-EHred-5-CH3-THF complex

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

Aminomethyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glycine cleavage system H protein

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

3a8i__assembly_1__model_1

3a8i__assembly_1__model_1 | I(q)

3a8i__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (10 domains)

CATH v4.4 (18 domains)

7. Citations (1)