4k3j

Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta

Method: X-RAY DIFFRACTION Dmax: 127.2 Å Quality: REASONABLE

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

Hepatocyte growth factor

Homo sapiens

UniProt P14210

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 495–721 Fragment:unp residues 495-721 Mutation:C604S Hepatocyte growth factor beta chain × 1 (P08581) Onartuzumab Fab heavy chain × 1 Onartuzumab Fab light chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.2;298 K;0.1 M sodium cacodylate pH 6.2, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.80 Å R-free 0.253

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.

35 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HGF_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–227; UniProt 495–721

Hepatocyte growth factor beta chain

Homo sapiens

UniProt P08581

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 39–564 Fragment:Sema and PSI domain, UNP residues 39-564 Hepatocyte growth factor × 1 (P14210) Onartuzumab Fab heavy chain × 1 Onartuzumab Fab light chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.2;298 K;0.1 M sodium cacodylate pH 6.2, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 2.80 Å R-free 0.253

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.

128 other PDB entries and 166 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MET_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–526; UniProt 39–564

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 4k3j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k3j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4k3j
Deposition date deposition_date2013-04-10
Structure title titleCrystal structure of Onartuzumab Fab in complex with MET and HGF-beta
Keywords keywordsantibody, glycosylation, Transferase-Immune System-Growth Factor complex; Transferase/Immune System/Growth Factor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.49
Radius of gyration Rg (electron density) rg_electron38.11
Forward intensity I(0) i0256750000.00
Molecular weight molecular_weight129330.0 kDa
Excluded volume excluded_volume161530 ų
Envelope volume envelope_volume217720 ų
Hydration-shell volume shell_volume48160 ų
Envelope diameter envelope_diameter135.0
Shell Rg shell_rg43.38
Envelope Rg envelope_rg37.87
Shape Rg shape_rg38.07
Total Rg total_rg38.56
Total atoms total_atoms9098
Residues n_residues1152
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 dmax127.2
Rg (real space) rg_real38.58
Rg uncertainty (real space) rg_real_error1.11
I(0) (real space) i0_real2.5670e+08
I(0) uncertainty (real space) i0_real_error3.9690e+06
Rg (reciprocal space) rg_reciprocal38.53
I(0) (reciprocal space) i0_reciprocal256700000.0000
Solution quality estimate total_estimate0.6917
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.4
Skewness Skewness skewness0.351
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23360000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.981; Smooth: 0.887

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4k3jA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4k3jA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4k3jB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id4k3jB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
Domain ID domain_id4k3jH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4k3jH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4k3jL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4k3jL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)