← Back to search
3eag

The crystal structure of UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (MPL) from Neisseria meningitides

Method: X-RAY DIFFRACTION
▼

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

UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase

Neisseria meningitidis MC58

UniProt Q9JRY9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 GLYCEROL × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3eag

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name Q9JRY9_NEIMB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–326； UniProt 1–323 Author chain B； PDBConstruct 4–326； UniProt 1–323

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3eag
Deposition date deposition_date2008-08-25
Structure title titleThe crystal structure of UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (MPL) from Neisseria meningitides
Keywords keywords;Neisseria meningitidis MC58, UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, ATP-binding, Ligase, Nucleotide-binding ;; LIGASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

3eag__assembly_1__model_1

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

Download this curve (.dat)

3eag__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3eag__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）28.26 Å
Rg (electron density)27.20 Å
Total Rg27.98 Å
Atom count4965
Residues632
Excluded volume88160 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3eag__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3eaga1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.5 — MurCD N-terminal domain
Superfamily Superfamily superfamilyc.5.1 — MurCD N-terminal domain
Family Family familyc.5.1.0 — automated matches
Domain ID domain_idd3eaga2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.2 — MurD-like peptide ligases, catalytic domain
Family Family familyc.72.2.0 — automated matches
Domain ID domain_idd3eaga3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3eagb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.5 — MurCD N-terminal domain
Superfamily Superfamily superfamilyc.5.1 — MurCD N-terminal domain
Family Family familyc.5.1.0 — automated matches
Domain ID domain_idd3eagb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.72 — Ribokinase-like
Superfamily Superfamily superfamilyc.72.2 — MurD-like peptide ligases, catalytic domain
Family Family familyc.72.2.0 — automated matches
Domain ID domain_idd3eagb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id3eagA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3eagA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily10 — Mur-like, catalytic domain
Domain ID domain_id3eagB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3eagB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily10 — Mur-like, catalytic domain
▶

7. Citations (1)