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)

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

t8E4 antibody Fab complexed with the active form of HGF

Umitsu, M., Kitago, Y., Takagi, J.

To be published.

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14210
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14210
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

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| 3D Structure

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 Query on 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), 0.297 (DCC)
R-Value Work: 0.248 (Depositor), 0.251 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Kitago, Y.

Umitsu, M.

Takagi, J.

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 (Full details and data files)

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