4O3T
Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP.14
- PDB DOI: https://doi.org/10.2210/pdb4O3T/pdb
- Classification: transferase/growth factor
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2013-12-18 Released: 2014-06-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.99 Å
- R-Value Free: 0.276 
- R-Value Work: 0.232 
- R-Value Observed: 0.233 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Hepatocyte growth factor | 240 | Homo sapiens | Mutation(s): 2  Gene Names: HGF, HPTA | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210 | |||||
PHAROS:  P14210 GTEx:  ENSG00000019991  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P14210 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Hepatocyte growth factor receptor | 551 | Homo sapiens | Mutation(s): 0  Gene Names: MET EC: 2.7.10.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581 | |||||
PHAROS:  P08581 GTEx:  ENSG00000105976  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P08581 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ZAP.14 | C [auth P] | 11 | synthetic construct | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | D [auth C] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1PE Query on 1PE | E [auth A] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.99 Å
- R-Value Free: 0.276 
- R-Value Work: 0.232 
- R-Value Observed: 0.233 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.789 | α = 90 |
b = 121.467 | β = 90 |
c = 137.657 | γ = 90 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
PHASER | phasing |
BUSTER | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-06-04  Deposition Author(s): Eigenbrot, C., Landgraf, K.E., Steffek, M.
Revision History (Full details and data files)
- Version 1.0: 2014-06-04
Type: Initial release - Version 1.1: 2014-07-02
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary