4D3C | pdb_00004d3c

Crystal structure of the NK1 domain of HGF in complex with anti-HGF monoclonal antibody SFN68.

• PDB DOI: https://doi.org/10.2210/pdb4D3C/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-21 Released: 2016-01-13 
• Deposition Author(s): Kang, Y.J., Kim, K.L., Cho, H.S., Chung, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Models: experimental

Literature

A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist.

Kang, Y.J., Kim, K.L., Cho, H.S., Chung, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 68.45 kDa 
• Atom Count: 4,247 
• Modelled Residue Count: 556 
• Deposited Residue Count: 626 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR	A	193	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210
PHAROS:  P14210 GTEx:  ENSG00000019991

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SFN68 FAB	B [auth H]	218	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SFN68 FAB	C [auth L]	215	Oryctolagus cuniculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834
Find proteins for U3KM01 (Oryctolagus cuniculus) Explore U3KM01  Go to UniProtKB:  U3KM01
UniProt Groups	U3KM01P01834

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.703	α = 90
b = 297.692	β = 90
c = 70.713	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Kang, Y.J., Kim, K.L., Cho, H.S., Chung, J.H.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary