3MKP

Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin

• PDB DOI: https://doi.org/10.2210/pdb3MKP/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2010-04-15 Released: 2010-08-18 
• Deposition Author(s): Gherardi, E., Chirgadze, D.Y., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Engineering a fragment of Hepatocyte Growth Factor/Scatter Factor for tissue and organ regeneration

Gherardi, E., Chirgadze, D.Y., Bocci, M., Brocchieri, C., Bevan, D., Kajstura, J., Esposito, G., Lietha, D., Rota, M., Leri, A., Mallorqui-Fernandez, N., Bandyopadhyay, A., Youles, M., Mulloy, B., Rowe, A., Alison, M., Edwards, D., Vannini, V., Blundell, T., Anversa, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.89 kDa 
• Atom Count: 5,766 
• Modelled Residue Count: 688 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A, B, C, D	183	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210
PHAROS:  P14210 GTEx:  ENSG00000019991

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	E	6		N/A
Glycosylation Resources
GlyTouCan:  G30141AL GlyCosmos:  G30141AL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SGN	H [auth A]	2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose C6 H13 N O11 S2 DQTRACMFIGDHSN-UKFBFLRUSA-N
EPE	G [auth A], J [auth B], L [auth C], N [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	F [auth A], I [auth B], K [auth C], M [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.73	α = 90
b = 129.73	β = 90
c = 118.19	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Gherardi, E., Chirgadze, D.Y., Blundell, T.L.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• 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: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary