SAXSdb — 6b88

▼

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

Signal peptidase I

Escherichia coli (strain K12)

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 78–324	Not recorded	CZD (8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；292 K；30% PEG 300, 0.1 M Sodium Acetate pH 4.5	Resolution 2.41 Å R-free 0.265
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 78–324	Not recorded	CZD (8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide × 1 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；292 K；30% PEG 300, 0.1 M Sodium Acetate pH 4.5	Resolution 2.41 Å R-free 0.265

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 6B88	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1B12 CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR Deposited 1999-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 77–324（248 aa） Fragment：CATALYTIC DOMAIN	Not recorded	1PN prop-2-en-1-yl (2S)-2-[(2S,3R)-3-(acetyloxy)-1-oxobutan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.95 Å R-free 0.246
1KN9 CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM. Deposited 2001-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–324（248 aa） Fragment：Residues 76-323, plus initiating methionine	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
1KN9 CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM. Deposited 2001-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 77–324（248 aa） Fragment：Residues 76-323, plus initiating methionine	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
1KN9 CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM. Deposited 2001-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 77–324（248 aa） Fragment：Residues 76-323, plus initiating methionine	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
1KN9 CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM. Deposited 2001-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 77–324（248 aa） Fragment：Residues 76-323, plus initiating methionine	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.278
1T7D Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor Deposited 2004-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–324（249 aa） Fragment：RESIDUES 76-324	Not recorded	M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.5% TRITON X-100, 15% PEG 4000, 20% PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 2.47 Å R-free 0.283
1T7D Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor Deposited 2004-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 76–324（249 aa） Fragment：RESIDUES 76-324	Not recorded	M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.5% TRITON X-100, 15% PEG 4000, 20% PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 2.47 Å R-free 0.283
3IIQ Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor Deposited 2009-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 77–324（248 aa） Fragment：UNP RESIDUES 76-323, PERIPLASMIC DOMAIN	Not recorded	JZA 4-[(1,1-dioxido-1,2-thiazetidin-2-yl)carbonyl]morpholine × 1 TRT FRAGMENT OF TRITON X-100 × 1 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K	Resolution 2.00 Å R-free 0.250
3IIQ Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor Deposited 2009-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–324（248 aa） Fragment：UNP RESIDUES 76-323, PERIPLASMIC DOMAIN	Not recorded	JZA 4-[(1,1-dioxido-1,2-thiazetidin-2-yl)carbonyl]morpholine × 1 TRT FRAGMENT OF TRITON X-100 × 1 GOL GLYCEROL × 4 CCN ACETONITRILE × 2 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K	Resolution 2.00 Å R-free 0.250
3S04 Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic Deposited 2011-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323	Not recorded	02U 14-methylhexadec-9-enoic acid × 1 RAM alpha-L-rhamnopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.265
3S04 Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic Deposited 2011-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323	Not recorded	02U 14-methylhexadec-9-enoic acid × 1 RAM alpha-L-rhamnopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.265
3S04 Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic Deposited 2011-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323 Chain B 76–324（249 aa） Fragment：Periplasmic domain, UNP residues 76-323	Not recorded	02U 14-methylhexadec-9-enoic acid × 2 RAM alpha-L-rhamnopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.265
9NLO Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–324（248 aa）	Mutation：P84A	EDO 1,2-ETHANEDIOL × 1 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline	Resolution 2.32 Å R-free 0.234
9NLO Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 77–324（248 aa）	Mutation：P84A	EDO 1,2-ETHANEDIOL × 1 M12 10-METHYLUNDECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294.15 K；25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline	Resolution 2.32 Å R-free 0.234

6 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 78–324 Author chain B； PDBConstruct 1–247； UniProt 78–324

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_id	6b88
Deposition date deposition_date	2017-10-05
Structure title title	E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)
Keywords keywords	Signal peptidase, SBDD, antibiotic, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex; HYDROLASE/HYDROLASE inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.76 Å
Radius of gyration Rg (electron density) rg_electron	25.67 Å
Forward intensity I(0) i0	47872900.00
Molecular weight molecular_weight	54433.0 kDa
Excluded volume excluded_volume	68355 Å³
Envelope volume envelope_volume	87378 Å³
Hydration-shell volume shell_volume	28275 Å³
Envelope diameter envelope_diameter	92.6 Å
Shell Rg shell_rg	33.28 Å
Envelope Rg envelope_rg	25.64 Å
Shape Rg shape_rg	25.66 Å
Total Rg total_rg	26.54 Å
Total atoms total_atoms	3845
Residues n_residues	479
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

▼

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

Maximum dimension Dmax dmax	92.2 Å
Rg (real space) rg_real	26.71 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	4.7870e+07
I(0) uncertainty (real space) i0_real_error	6.9750e+05
Rg (reciprocal space) rg_reciprocal	26.73 Å
I(0) (reciprocal space) i0_reciprocal	47870000.0000
Solution quality estimate total_estimate	0.8809
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.7 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.542
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10350000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Signal peptidase I
Molecular weight formula_weight	27736.3 kDa
EC 编号 ec_number	3.4.21.89
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	3947

RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide ;
Molecular weight formula_weight	892.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6b88a_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

Domain ID domain_id	d6b88b_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

CATH v4.4 (4 domains)

Domain ID domain_id	6b88A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	6b88A02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6b88B01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	6b88B02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	109.980 Å
Unit-cell length b length_b	109.980 Å
Unit-cell length c length_c	116.250 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	16

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.407 Å
Low-resolution limit resolution_low	54.990 Å
R factor r_factor	0.2397
R_work r_work	0.2384
R_free r_free	0.2646

fit	/app/data/saxs_computation/b8/6b88/6b88.fit
pddf	/app/data/pr_computation/b8/6b88/6b88.pr.out
profile	/app/data/saxs_computation/b8/6b88/6b88.dat

E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)

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

Signal peptidase I

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