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1mpl

CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE

Method: X-RAY DIFFRACTION Dmax: 61.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-alanyl-D-alanine carboxypeptidase

OrganismNot specified

UniProt P15555

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 32–380 Fragment：DD-Peptidase RE1 GLYCYL-L-A-AMINOPIMELYL-E-(D-2-AMINOETHYL)PHOSPHONATE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 8000, SODIUM PHOSPHATE, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.12 Å R-free 0.140

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1MPL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CEF CEFOTAXIME COMPLEXED WITH THE STREPTOMYCES R61 DD-PEPTIDASE Deposited 1995-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.04 Å R-free 0.240
1CEG CEPHALOTHIN COMPLEXED WITH DD-PEPTIDASE Deposited 1995-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded CEP CEPHALOTHIN GROUP × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å R-free 0.212
1HVB CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN Deposited 2001-01-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded CEH 5-{3-(S)-(4-(R)-ACETYLAMINO-4-CARBOXY-BUTYRYLAMINO)-3-[1-(R)-(1-(R)-CARBOXY-ETHYLCARBAMOYL)-ETHYLCARBAMOYL]-PROPYL}-2-( CARBOXY-PHENYLACETYLAMINO-METHYL)-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 8000, sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.17 Å R-free 0.153
1IKG MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT Deposited 2001-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded REX GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANYL-D-ALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；PEG 8000, SODIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Resolution 1.90 Å R-free 0.184
1IKI COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT Deposited 2001-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded REY GLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANINE × 1 DAL D-ALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；PEG 8000, SODIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 1.25 Å R-free 0.154
1PW1 Non-Covalent Complex Of Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin Deposited 2003-06-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa） Fragment：DD-PEPTIDASE
Not recorded HEL (2S,5R,6R)-6-{[(6R)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLATE × 1 GOL GLYCEROL × 3 FOR FORMYL GROUP × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM Sodium Phosphate, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.151
1PW8 Covalent Acyl Enzyme Complex Of The R61 DD-Peptidase with A Highly Specific Cephalosporin Deposited 2003-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa） Fragment：DD-PEPTIDASE
Not recorded H2A (6R,7R)-3-[(ACETYLOXY)METHYL]-7-{[(6S)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-8-OXO-5-THIA-1-AZABICYCLO[4.2.0]OCTANE-2-CARBOXYLATE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM Sodium Phosphate, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.30 Å R-free 0.150
1PWC penicilloyl acyl enzyme complex of the Streptomyces R61 DD-peptidase with penicillin G Deposited 2003-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa） Fragment：DD-PEPTIDASE
Not recorded PNM OPEN FORM - PENICILLIN G × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM Sodium Phosphate, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.10 Å R-free 0.148
1PWD Covalent acyl enzyme complex of the Streptomyces R61 DD-peptidase with cephalosporin C Deposited 2003-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa） Fragment：DD-PEPTIDASE
Not recorded 0MU (2R)-5-(acetyloxymethyl)-2-[(1R)-1-[[(5R)-5-azanyl-6-oxidanyl-6-oxidanylidene-hexanoyl]amino]-2-oxidanylidene-ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM Sodium Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.20 Å R-free 0.166
1PWG Covalent Penicilloyl Acyl Enzyme Complex Of The Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin Deposited 2003-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa） Fragment：DD-PEPTIDASE
Not recorded HE0 (2R,4S)-2-[(1R)-1-{[(6S)-6-carboxy-6-(glycylamino)hexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM Sodium Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.07 Å R-free 0.146
1SCW TOWARD BETTER ANTIBIOTICS: CRYSTAL STRUCTURE OF R61 DD-PEPTIDASE INHIBITED BY A NOVEL MONOCYCLIC PHOSPHATE INHIBITOR Deposited 2004-02-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded CP5 (2Z)-3-{[OXIDO(OXO)PHOSPHINO]OXY}-2-PHENYLACRYLATE × 1 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.13 Å R-free 0.143
1SDE Toward Better Antibiotics: Crystal Structure Of D-Ala-D-Ala Peptidase inhibited by a novel bicyclic phosphate inhibitor Deposited 2004-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–378（347 aa）
Not recorded 2PB 2-[(DIOXIDOPHOSPHINO)OXY]BENZOATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.15 Å R-free 0.140
1YQS Inhibition of the R61 DD-Peptidase by N-benzoyl-beta-sultam Deposited 2005-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa） Fragment：DD-PEPTIDASE
Not recorded BSA 2-(BENZOYLAMINO)ETHANESULFONIC ACID × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；20% PEG 8000, 50mM sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.05 Å R-free 0.136
3PTE THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6 A RESOLUTION Deposited 1994-08-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–380（349 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.211

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DAC_STRSR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–349； UniProt 32–380

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1mpl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1mpl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1mpl
Deposition date deposition_date2002-09-12
Structure title titleCRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE
Keywords keywordsTRANSITION STATE ANALOG, PEPTIDOGLYCAN, PENICILLIN BINDING PROTEIN, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.91 Å
Radius of gyration Rg (electron density) rg_electron18.78 Å
Forward intensity I(0) i025400000.00
Molecular weight molecular_weight37745.0 kDa
Excluded volume excluded_volume46791 ų
Envelope volume envelope_volume50965 ų
Hydration-shell volume shell_volume21914 ų
Envelope diameter envelope_diameter63.1 Å
Shell Rg shell_rg25.84 Å
Envelope Rg envelope_rg19.08 Å
Shape Rg shape_rg18.76 Å
Total Rg total_rg19.69 Å
Total atoms total_atoms2652
Residues n_residues345
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.2 Å
Rg (real space) rg_real19.75 Å
Rg uncertainty (real space) rg_real_error0.23 Å
I(0) (real space) i0_real2.5400e+07
I(0) uncertainty (real space) i0_real_error2.6490e+05
Rg (reciprocal space) rg_reciprocal19.77 Å
I(0) (reciprocal space) i0_reciprocal25400000.0000
Solution quality estimate total_estimate0.9015
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.0 Å
Skewness Skewness skewness0.125
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6089000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1mpla_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id1mplA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
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8. Citations (3)

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9. Files and Curves (10)