4ihf

Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production

Method: X-RAY DIFFRACTION

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

UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Acyl carrier protein × 3 （G7RM21） CHLORIDE ION × 1 S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate × 3 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Acyl carrier protein × 3 （G7RM21） CHLORIDE ION × 1 S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate × 3 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Acyl carrier protein × 6 （G7RM21） CHLORIDE ION × 2 S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LPXD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–348； UniProt 3–341 Author chain B； PDBConstruct 10–348； UniProt 3–341 Author chain C； PDBConstruct 10–348； UniProt 3–341 Author chain D； PDBConstruct 10–348； UniProt 3–341 Author chain E； PDBConstruct 10–348； UniProt 3–341 Author chain F； PDBConstruct 10–348； UniProt 3–341

Acyl carrier protein

Escherichia coli

UniProt G7RM21

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase × 3 （P21645） CHLORIDE ION × 1 S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate × 3 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase × 3 （P21645） CHLORIDE ION × 1 S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate × 3 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase × 6 （P21645） CHLORIDE ION × 2 S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G7RM21_ECOC1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 3–80； UniProt 1–78 Author chain H； PDBConstruct 3–80； UniProt 1–78 Author chain I； PDBConstruct 3–80； UniProt 1–78 Author chain J； PDBConstruct 3–80； UniProt 1–78 Author chain K； PDBConstruct 3–80； UniProt 1–78 Author chain L； PDBConstruct 3–80； UniProt 1–78

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	4ihf
Deposition date deposition_date	2012-12-18
Structure title title	Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production
Keywords keywords	;Acyl Carrier Protein, Left Handed Beta Helix, LpxD, acyltransferase, Lipid A, Protein-Protein complex, ACP Recognition Domain, ACP mediated product release, TRANSFERASE-LIPID BINDING PROTEIN complex ;; TRANSFERASE/LIPID BINDING 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.

4ihf__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4ihf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ihf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	33.09 Å
Rg (electron density)	32.08 Å
Total Rg	32.59 Å
Atom count	9191
Residues	1223
Excluded volume	164230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ihf__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ihf__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ihf__assembly_3__model_1`	dodecameric （12）	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	UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
Molecular weight formula_weight	36864.2 kDa
EC 编号 ec_number	2.3.1.191
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	19412

MGHHHHHHASIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAANVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD

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	Acyl carrier protein
Molecular weight formula_weight	8870.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

SHMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	885275
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (3R)-3-hydroxytetradecanethioate
Molecular weight formula_weight	584.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	920

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4ihfg_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d4ihfh_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d4ihfi_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d4ihfj_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d4ihfk_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d4ihfl_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

CATH v4.4 (12 domains)

Domain ID domain_id	4ihfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	4ihfA02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	4ihfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	4ihfB02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	4ihfC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	4ihfC02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	4ihfD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	4ihfD02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	4ihfE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	4ihfE02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	4ihfF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	4ihfF02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	84.299 Å
Unit-cell length b length_b	89.441 Å
Unit-cell length c length_c	112.251 Å
Unit-cell angle α angle_alpha	104.06 °
Unit-cell angle β angle_beta	92.40 °
Unit-cell angle γ angle_gamma	118.47 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	43.380 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	0.2160

Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production

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

UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Acyl carrier 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

4ihf__assembly_2__model_1

4ihf__assembly_2__model_1 | I(q)

4ihf__assembly_2__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 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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production

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

UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acyl carrier 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

4ihf__assembly_2__model_1

4ihf__assembly_2__model_1 | I(q)

4ihf__assembly_2__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 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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)