1p31

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae

Method: X-RAY DIFFRACTION

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

UDP-N-acetylmuramate--alanine ligase

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURC_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain B； PDBConstruct 1–475； UniProt 1–475

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	1p31
Deposition date deposition_date	2003-04-16
Structure title title	Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae
Keywords keywords	alpha/beta protein, 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.

1p31__assembly_1__model_1

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

Download this curve (.dat)

1p31__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1p31__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.33 Å
Rg (electron density)	22.42 Å
Total Rg	23.14 Å
Atom count	3594
Residues	449
Excluded volume	63982 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1p31__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1p31__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylmuramate--alanine ligase
Molecular weight formula_weight	52760.6 kDa
EC 编号 ec_number	6.3.2.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7928

MKHSHEEIRKIIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQMLAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESWKN

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
Molecular weight formula_weight	677.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	700

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1p31a1
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.5.1.1 — MurCD N-terminal domain

Domain ID domain_id	d1p31a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.59 — MurD-like peptide ligases, peptide-binding domain
Superfamily Superfamily superfamily	c.59.1 — MurD-like peptide ligases, peptide-binding domain
Family Family family	c.59.1.1 — MurCDEF C-terminal domain

Domain ID domain_id	d1p31a3
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.72.2.1 — MurCDEF

Domain ID domain_id	d1p31b1
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.5.1.1 — MurCD N-terminal domain

Domain ID domain_id	d1p31b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.59 — MurD-like peptide ligases, peptide-binding domain
Superfamily Superfamily superfamily	c.59.1 — MurD-like peptide ligases, peptide-binding domain
Family Family family	c.59.1.1 — MurCDEF C-terminal domain

Domain ID domain_id	d1p31b3
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.72.2.1 — MurCDEF

CATH v4.4 (6 domains)

Domain ID domain_id	1p31A01
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	1p31A02
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	1p31A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	20 — Mur ligase, C-terminal domain

Domain ID domain_id	1p31B01
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	1p31B02
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	1p31B03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	20 — Mur ligase, C-terminal domain

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Unit-cell length a length_a	91.523 Å
Unit-cell length b length_b	92.274 Å
Unit-cell length c length_c	118.174 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	8

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1714
R_work r_work	0.1694
R_free r_free	0.2084

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae

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

UDP-N-acetylmuramate--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

1p31__assembly_1__model_1

1p31__assembly_1__model_1 | I(q)

1p31__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae

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

UDP-N-acetylmuramate--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

1p31__assembly_1__model_1

1p31__assembly_1__model_1 | I(q)

1p31__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)