3shi

Crystal structure of human MMP1 catalytic domain at 2.2 A resolution

Method: X-RAY DIFFRACTION Dmax: 105.6 Å Quality: GOOD

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

Interstitial collagenase

Homo sapiens

UniProt P03956

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 106–261 Fragment:UNP residues 106-261 ZN ZINC ION × 2 CA CALCIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;30% PEG8000, 0.1 M Tris-HCl, pH 8.5 Resolution 2.20 Å R-free 0.278
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 106–261 Fragment:UNP residues 106-261 ZN ZINC ION × 2 CA CALCIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;30% PEG8000, 0.1 M Tris-HCl, pH 8.5 Resolution 2.20 Å R-free 0.278
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain M; UniProt 106–261 Fragment:UNP residues 106-261 ZN ZINC ION × 2 CA CALCIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;30% PEG8000, 0.1 M Tris-HCl, pH 8.5 Resolution 2.20 Å R-free 0.278

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.

13 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MMP1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–156; UniProt 106–261 Author chain G; PDBConstruct 1–156; UniProt 106–261 Author chain M; PDBConstruct 1–156; UniProt 106–261

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 3shi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3shi
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3shi
Deposition date deposition_date2011-06-16
Structure title titleCrystal structure of human MMP1 catalytic domain at 2.2 A resolution
Keywords keywords;matrix metalloproteinase, paramagnetic restraints, paramagnetic tag, lanthanides, protein refinement, residual dipolar couplings, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.80
Radius of gyration Rg (electron density) rg_electron30.58
Forward intensity I(0) i050580400.00
Molecular weight molecular_weight53031.0 kDa
Excluded volume excluded_volume64757 ų
Envelope volume envelope_volume83199 ų
Hydration-shell volume shell_volume24637 ų
Envelope diameter envelope_diameter105.3
Shell Rg shell_rg34.66
Envelope Rg envelope_rg30.27
Shape Rg shape_rg30.56
Total Rg total_rg30.99
Total atoms total_atoms3723
Residues n_residues468
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax105.6
Rg (real space) rg_real31.11
Rg uncertainty (real space) rg_real_error1.26
I(0) (real space) i0_real5.0580e+07
I(0) uncertainty (real space) i0_real_error8.9150e+05
Rg (reciprocal space) rg_reciprocal30.98
I(0) (reciprocal space) i0_reciprocal50580000.0000
Solution quality estimate total_estimate0.7888
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary22.8
Skewness Skewness skewness0.467
Kurtosis Kurtosis kurtosis-0.527
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18920000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.663; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.438; Smooth: 0.822

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3shia_
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.92.1.11 — Matrix metalloproteases, catalytic domain
Domain ID domain_idd3shig_
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.92.1.11 — Matrix metalloproteases, catalytic domain
Domain ID domain_idd3shim_
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.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id3shiA00
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_id3shiG00
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_id3shiM00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)

8. Citations (4)

9. Files and Curves (10)