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6ht9

Mouse fetuin-B in complex with crayfish astacin

Method: X-RAY DIFFRACTION Dmax: 131.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Astacin

OrganismNot specified

UniProt P07584

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–251 Not recorded Fetuin-B × 1 （Q9QXC1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6. Resolution 3.10 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–251 Not recorded Fetuin-B × 1 （Q9QXC1） ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6. Resolution 3.10 Å R-free 0.270

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 6HT9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AST STRUCTURE OF ASTACIN AND IMPLICATIONS FOR ACTIVATION OF ASTACINS AND ZINC-LIGATION OF COLLAGENASES Deposited 1993-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1IAA CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY Deposited 1994-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa）
Not recorded CU COPPER (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1IAB CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY Deposited 1994-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa）
Not recorded CO COBALT (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.79 Å
1IAC REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON WITH THERMOLYSIN Deposited 1994-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa）
Not recorded HG MERCURY (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1IAD REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON TO THERMOLYSIN Deposited 1994-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1IAE CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY Deposited 1994-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa）
Not recorded NI NICKEL (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.83 Å
1QJI Structure of astacin with a transition-state analogue inhibitor Deposited 1999-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 50–249（200 aa） Fragment：CATALYTIC DOMAIN
Not recorded ZN ZINC ION × 1 PKF CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE
Resolution 2.14 Å
1QJJ Structure of astacin with a hydroxamic acid inhibitor Deposited 1999-06-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 50–249（200 aa） Fragment：CATALYTIC DOMAIN
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE
Resolution 1.86 Å
3LQ0 Zymogen structure of crayfish astacin metallopeptidase Deposited 2010-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 16–250（235 aa）
Mutation：I91L,E93A ZN ZINC ION × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；For crystallization, reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Innovadyne) by a Cartesian (Genomic Solutions) nanodrop robot at the High-Throughput Crystallography Platform of the Barcelona Science Park. Best crystals appeared in a Bruker steady-temperature crystal farm at 4C with protein solution (10 mg/mL in 50mM AMPSO pH9.0) and 20% PEG 8000, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6 as reservoir solution. These conditions were efficiently scaled up to the microliter range with 24-well Cryschem crystallization dishes (Hampton Research). Crystals were cryo-protected with 16% PEG 8000, 20% glycerol, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.45 Å R-free 0.180
6SAZ Cleaved human fetuin-b in complex with crayfish astacin Deposited 2019-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 50–251（202 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.
Resolution 3.00 Å R-free 0.247
6SAZ Cleaved human fetuin-b in complex with crayfish astacin Deposited 2019-07-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 50–251（202 aa）
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.
Resolution 3.00 Å R-free 0.247

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ASTA_ASTAS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–251； UniProt 1–251 Author chain C； PDBConstruct 1–251； UniProt 1–251

Fetuin-B

Mus musculus

UniProt Q9QXC1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 19–388 Not recorded Astacin × 1 （P07584） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6. Resolution 3.10 Å R-free 0.270
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 19–388 Not recorded Astacin × 1 （P07584） ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6. Resolution 3.10 Å R-free 0.270

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 6HT9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6HPV Crystal structure of mouse fetuin-B Deposited 2018-09-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–388（370 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；150 mM NaCl, 100 mM NaOAc, 20 mM Na-HEPES pH 7.8, 25% PEG 4000, 8% isopropanol
Resolution 2.30 Å R-free 0.253
7AUW Inhibitory complex of human meprin beta with mouse fetuin-B. Deposited 2020-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–388（388 aa）
Chain D 1–388（388 aa）
Not recorded NA SODIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；293 K；20.0% PEG smear medium, 0.1M ammonium sulfate, 0.05M magnesium sulfate heptahydrate, 0.1M bicine pH 9.3, 10% ethylene glycol.
Resolution 2.80 Å R-free 0.261

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FETUB_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–370； UniProt 19–388 Author chain D； PDBConstruct 1–370； UniProt 19–388

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 6ht9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ht9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ht9
Deposition date deposition_date2018-10-03
Structure title titleMouse fetuin-B in complex with crayfish astacin
Keywords keywordspeptidase inhibitor, metallopeptidase, astacin, ovastacin inhibitor, fetuin, cystatin, 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_guinier40.17 Å
Radius of gyration Rg (electron density) rg_electron40.29 Å
Forward intensity I(0) i0205012000.00
Molecular weight molecular_weight113760.0 kDa
Excluded volume excluded_volume141020 ų
Envelope volume envelope_volume202820 ų
Hydration-shell volume shell_volume42948 ų
Envelope diameter envelope_diameter133.7 Å
Shell Rg shell_rg44.20 Å
Envelope Rg envelope_rg40.35 Å
Shape Rg shape_rg40.30 Å
Total Rg total_rg40.49 Å
Total atoms total_atoms7989
Residues n_residues1015
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 dmax131.0 Å
Rg (real space) rg_real40.32 Å
Rg uncertainty (real space) rg_real_error1.11 Å
I(0) (real space) i0_real2.0500e+08
I(0) uncertainty (real space) i0_real_error3.5790e+06
Rg (reciprocal space) rg_reciprocal40.17 Å
I(0) (reciprocal space) i0_reciprocal205000000.0000
Solution quality estimate total_estimate0.8613
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.3 Å
Skewness Skewness skewness0.337
Kurtosis Kurtosis kurtosis-0.730
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17140000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.795; Smooth: 0.781
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6ht9a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.8 — Astacin
Domain ID domain_idd6ht9c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.8 — Astacin

CATH v4.4 (4 domains)

Domain ID domain_id6ht9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id6ht9B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily10 —
Domain ID domain_id6ht9C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id6ht9D01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)