SAXSdb — 1hvb

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

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

OrganismNot specified

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	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

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 1HVB	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 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 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
1IKG MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT Deposited 2001-05-03	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 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
1MPL CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE Deposited 2002-09-12	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） Fragment：DD-Peptidase	Not recorded	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
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 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 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hvb
Deposition date deposition_date	2001-01-08
Structure title title	CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN
Keywords keywords	Protein-cephalosporin complex, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.90 Å
Radius of gyration Rg (electron density) rg_electron	18.75 Å
Forward intensity I(0) i0	25450700.00
Molecular weight molecular_weight	37783.0 kDa
Excluded volume excluded_volume	46827 Å³
Envelope volume envelope_volume	51286 Å³
Hydration-shell volume shell_volume	22109 Å³
Envelope diameter envelope_diameter	60.8 Å
Shell Rg shell_rg	25.83 Å
Envelope Rg envelope_rg	19.02 Å
Shape Rg shape_rg	18.73 Å
Total Rg total_rg	19.67 Å
Total atoms total_atoms	2930
Residues n_residues	346
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.7 Å
Rg (real space) rg_real	19.74 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	2.5450e+07
I(0) uncertainty (real space) i0_real_error	2.8490e+05
Rg (reciprocal space) rg_reciprocal	19.76 Å
I(0) (reciprocal space) i0_reciprocal	25450000.0000
Solution quality estimate total_estimate	0.9049
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.118
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6449000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
Molecular weight formula_weight	37422.6 kDa
EC 编号 ec_number	3.4.16.4
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3590

ADLPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAITTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITVRQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNAPGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPDTVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFSALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTVQGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKPTT

Entity 2 Entity 2 non-polymer

Description description	;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 ;
Molecular weight formula_weight	750.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	555

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1hvba_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id	1hvbA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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8. Citations (3)

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Unit-cell length a length_a	50.778 Å
Unit-cell length b length_b	66.664 Å
Unit-cell length c length_c	100.928 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	4

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

Resolution resolution	1.170 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1141
R_work r_work	0.1126
R_free r_free	0.1528

fit	/app/data/saxs_computation/hv/1hvb/1hvb.fit
pddf	/app/data/pr_computation/hv/1hvb/1hvb.pr.out
profile	/app/data/saxs_computation/hv/1hvb/1hvb.dat

CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN

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

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction