SAXSdb — 8v3n

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

Cytosolic carboxypeptidase-like protein 5

Homo sapiens

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 2–338 Chain A； UniProt 425–605	Mutation：E516A,residues 339-424 replaced with a SGSGG loop	ZN ZINC ION × 1 MLT D-MALATE × 2 A1AAG (2S)-2-{[(S)-[(3S)-3-acetamido-4-(ethylamino)-4-oxobutyl](hydroxy)phosphoryl]methyl}pentanedioic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550	Resolution 2.30 Å R-free 0.222

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 8V3N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8V3M CCP5 apo structure Deposited 2023-11-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–338（337 aa） Chain A 425–605（181 aa）	Mutation：E516A,residues 339-424 replaced with a SGSGG loop Mutation：E516A,residues 339-424 replaced with a SGSGG loop	MLT D-MALATE × 2 IMD IMIDAZOLE × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550	Resolution 1.80 Å R-free 0.201
8V3O CCP5 in complex with Glu-P-peptide 1 transition state analog Deposited 2023-11-28	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–338（337 aa） Chain A 425–605（181 aa）	Mutation：E516A,residues 339-424 replaced with a SGSGG loop Mutation：E516A,residues 339-424 replaced with a SGSGG loop	ZN ZINC ION × 1 MLT D-MALATE × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550	Resolution 2.30 Å R-free 0.227
8V3P CCP5 in complex with Glu-P-peptide 2 transition state analog Deposited 2023-11-28	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–338（337 aa） Chain A 425–605（181 aa）	Mutation：E516A,construct is from residues 2-605,with residues 339-424 replaced with a SGSGG loop Mutation：E516A,construct is from residues 2-605,with residues 339-424 replaced with a SGSGG loop	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550	Resolution 2.36 Å R-free 0.225
8V3Q Structure of CCP5 class1 Deposited 2023-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–605（604 aa） Fragment：residues 2-605	Mutation：E516A	ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8V3R Structure of CCP5 class2 Deposited 2023-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–605（604 aa） Fragment：residues 2-605	Mutation：E516A	ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8V3S Structure of CCP5 class3 Deposited 2023-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–605（604 aa） Fragment：residues 2-605	Mutation：E516A	ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8V4K CCP5 in complex with microtubules class1 Deposited 2023-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 2–605（604 aa） Fragment：residues 2-605	Mutation：E516A	MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8V4L CCP5 in complex with microtubules class2 Deposited 2023-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: hexameric	Chain E 2–605（604 aa） Fragment：residues 2-605	Mutation：E516A	MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 GLU GLUTAMIC ACID × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8V4M CCP5 in complex with microtubules class3 Deposited 2023-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: hexameric	Chain E 2–605（604 aa） Fragment：residues 2-605	Mutation：E516A	MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 GLU GLUTAMIC ACID × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBPC5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–338； UniProt 2–338 Author chain A； PDBConstruct 344–524； UniProt 425–605

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	8v3n
Deposition date deposition_date	2023-11-28
Structure title title	CCP5 in complex with Glu-P-Glu transition state analog
Keywords keywords	carboxypeptidase deglutamylation branch glutamate removal microtubule, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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	23.96 Å
Radius of gyration Rg (electron density) rg_electron	22.94 Å
Forward intensity I(0) i0	52283700.00
Molecular weight molecular_weight	55344.0 kDa
Excluded volume excluded_volume	68717 Å³
Envelope volume envelope_volume	78183 Å³
Hydration-shell volume shell_volume	27939 Å³
Envelope diameter envelope_diameter	78.5 Å
Shell Rg shell_rg	30.66 Å
Envelope Rg envelope_rg	23.32 Å
Shape Rg shape_rg	22.94 Å
Total Rg total_rg	23.80 Å
Total atoms total_atoms	3899
Residues n_residues	489
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	75.5 Å
Rg (real space) rg_real	23.87 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	5.2280e+07
I(0) uncertainty (real space) i0_real_error	6.3490e+05
Rg (reciprocal space) rg_reciprocal	23.89 Å
I(0) (reciprocal space) i0_reciprocal	52280000.0000
Solution quality estimate total_estimate	0.9028
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	74.3 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.401
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9795000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Cytosolic carboxypeptidase-like protein 5
Molecular weight formula_weight	59170.7 kDa
EC 编号 ec_number	3.4.17.-,3.4.17.24
Mutation mutation	E516A,residues 339-424 replaced with a SGSGG loop
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4123

NELRCGGLLFSSRFDSGNLAHVEKVESLSSDGEGVGGGASALTSGIASSPDYEFNVWTRPDCAETEFENGNRSWFYFSVRGGMPGKLIKINIMNMNKQSKLYSQGMAPFVRTLPTRPRWERIRDRPTFEMTETQFVLSFVHRFVEGRGATTFFAFCYPFSYSDCQELLNQLDQRFPENHPTHSSPLDTIYYHRELLCYSLDGLRVDLLTITSCHGLREDREPRLEQLFPDTSTPRPFRFAGKRIFFLSSRVHPGETPSSFVFNGFLDFILRPDDPRAQTLRRLFVFKLIPMLNPDGVVRGHYRTDSRGVNLNRQYLKPDAVLHPAIYGAKAVLLYHHVSGSGGSGVAYYVDLHGHASKRGCFMYGNSFSDESTQVENMLYPKLISLNSAHFDFQGCNFSEKNMYARDRRDGQSKEGSGRVAIYKASGIIHSYTLACNYNTGRSVNSIPAACHDNGRASPPPPPAFPSRYTVELFEQVGRAMAIAALDMAECNPWPRIVLSEHSSLTNLRAWMLKHVRNSRGLSS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(2S)-2-{[(S)-[(3S)-3-acetamido-4-(ethylamino)-4-oxobutyl](hydroxy)phosphoryl]methyl}pentanedioic acid
Molecular weight formula_weight	380.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

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8. Citations (1)

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Unit-cell length a length_a	65.114 Å
Unit-cell length b length_b	80.414 Å
Unit-cell length c length_c	103.229 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	65.110 Å
R factor r_factor	0.1945
R_work r_work	0.1930
R_free r_free	0.2218

fit	/app/data/saxs_computation/v3/8v3n/8v3n.fit
pddf	/app/data/pr_computation/v3/8v3n/8v3n.pr.out
profile	/app/data/saxs_computation/v3/8v3n/8v3n.dat

CCP5 in complex with Glu-P-Glu transition state analog

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

Cytosolic carboxypeptidase-like protein 5

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