9L7E | pdb_00009l7e

Crystal structure of human kinesin-1 motor domain (G234A mutant) in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb9L7E/pdb

Classification: MOTOR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-12-26 Released: 2025-04-23
Deposition Author(s): Makino, T., Miyazono, K., Tanokura, M., Tomishige, M.
Funding Organization(s): Human Frontier Science Program (HFSP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.252 (Depositor), 0.247 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping

Makino, T., Kanada, R., Mori, T., Miyazono, K.I., Komori, Y., Yanagisawa, H., Takada, S., Tanokura, M., Kikkawa, M., Tomishige, M.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.09.19.613825

Macromolecule Content

Total Structure Weight: 40.47 kDa
Atom Count: 2,445
Modelled Residue Count: 300
Deposited Residue Count: 355
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-1 heavy chain	A	355	Homo sapiens	Mutation(s): 1 Gene Names: KIF5B, KNS, KNS1
UniProt & NIH Common Fund Data Resources
Find proteins for P33176 (Homo sapiens) Explore P33176 Go to UniProtKB: P33176
PHAROS: P33176 GTEx: ENSG00000170759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33176
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252 (Depositor), 0.247 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.36	α = 90
b = 67.93	β = 96.05
c = 55.45	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Human Frontier Science Program (HFSP)	France	RGY62/2006

Revision History (Full details and data files)

Version 1.0: 2025-04-23
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.