6LZ9 | pdb_00006lz9

t8E4 antibody Fab complexed with the active form of HGF

• PDB DOI: https://doi.org/10.2210/pdb6LZ9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Homo sapiens, hybrid
• Mutation(s): Yes 


• Deposited: 2020-02-18 Released: 2020-03-11 
• Deposition Author(s): Kitago, Y., Umitsu, M., Takagi, J.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Models: experimental

Literature

t8E4 antibody Fab complexed with the active form of HGF

Umitsu, M., Kitago, Y., Takagi, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 87.31 kDa 
• Atom Count: 5,028 
• Modeled Residue Count: 661 
• Deposited Residue Count: 787 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A	108	Homo sapiens	Mutation(s): 5  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	B	242	Homo sapiens	Mutation(s): 3  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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of t8E4 Fab fragment	C [auth H]	223	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of t8E4 Fab fragment	D [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	C [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.18	α = 90
b = 176.18	β = 90
c = 122.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Kitago, Y., Umitsu, M., Takagi, J.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	19am0101075
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP17H01420

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary