5vvw

Structure of MurC from Pseudomonas aeruginosa

Method: X-RAY DIFFRACTION

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

UDP-N-acetylmuramate--L-alanine ligase

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 5 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURC_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–315； UniProt 16–322 Author chain B； PDBConstruct 9–315； UniProt 16–322 Author chain C； PDBConstruct 9–315； UniProt 16–322 Author chain D； PDBConstruct 9–315； UniProt 16–322 Author chain E； PDBConstruct 9–315； UniProt 16–322 Author chain F； PDBConstruct 9–315； UniProt 16–322 Author chain G； PDBConstruct 9–315； UniProt 16–322 Author chain H； PDBConstruct 9–315； UniProt 16–322

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	5vvw
Deposition date deposition_date	2017-05-21
Structure title title	Structure of MurC from Pseudomonas aeruginosa
Keywords keywords	;MurC, Pseudomonas aeruginosa, SSGCID, Beryllium, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, LIGASE ;; LIGASE
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.

5vvw__assembly_1__model_1

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

Download this curve (.dat)

5vvw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vvw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.58 Å
Rg (electron density)	31.41 Å
Total Rg	32.12 Å
Atom count	8995
Residues	1220
Excluded volume	159820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vvw__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vvw__assembly_2__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylmuramate--L-alanine ligase
Molecular weight formula_weight	33845.4 kDa
EC 编号 ec_number	6.3.2.8
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	19018

MAHHHHHHRRIHFVGIGGAGMCGIAEVLLNLGYEVSGSDLKASAVTERLEKFGAQIFIGHQAENADGADVLVVSSAINRANPEVASALERRIPVVPRAEMLAELMRYRHGIAVAGTHGKTTTTSLIASVFAAGGLDPTFVIGGRLNAAGTNAQLGASRYLVAEADESDASFLHLQPMVAVVTNIDADHMATYGGDFNKLKKTFVEFLHNLPFYGLAVMCVDDPVVREILPQIARPTVTYGLSEDADVRAINIRQEGMRTWFTVLRPEREPLDVSVNMPGLHNVLNSLATIVIATDEGISDEAIVQGLSGFQGVGR

Source Source

Source organism organism	Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	877

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d5vvwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwe3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwf3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwg1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwg3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5vvwh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.5 — MurCD N-terminal domain
Superfamily Superfamily superfamily	c.5.1 — MurCD N-terminal domain
Family Family family	c.5.1.0 — automated matches

Domain ID domain_id	d5vvwh2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.0 — automated matches

Domain ID domain_id	d5vvwh3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id	5vvwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	5vvwH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5vvwH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

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Unit-cell length a length_a	284.820 Å
Unit-cell length b length_b	109.400 Å
Unit-cell length c length_c	108.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.812 Å
R factor r_factor	0.1890
R_work r_work	0.1888
R_free r_free	0.2030

Structure of MurC from Pseudomonas aeruginosa

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

UDP-N-acetylmuramate--L-alanine ligase

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

5vvw__assembly_1__model_1

5vvw__assembly_1__model_1 | I(q)

5vvw__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) 40 domains

SCOP 2.08 (24 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Structure of MurC from Pseudomonas aeruginosa

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

UDP-N-acetylmuramate--L-alanine ligase

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

5vvw__assembly_1__model_1

5vvw__assembly_1__model_1 | I(q)

5vvw__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) 40 domains

SCOP 2.08 (24 domains)

CATH v4.4 (16 domains)

7. Citations (1)