4FOI | pdb_00004foi

Crystal Structure of recombinant human Hexokinase type I mutant D413N with Glucose 1,6-bisphosphate

PDB DOI: https://doi.org/10.2210/pdb4FOI/pdb

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

Deposited: 2012-06-20 Released: 2013-07-03
Deposition Author(s): Shen, L., Honzatko, R.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.247 (Depositor), 0.240 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DETERMINATION of SITE AFFINITY CONSTANTS FOR PRODUCT INHIBITION OF WILD-TYPE AND MUTANT FORMS OF RECOMBINANT HUMAN HEXOKINASE TYPE I

Shen, L., Gao, Y., Honzatko, R.B.

To be published.

Macromolecule Content

Total Structure Weight: 207.8 kDa
Atom Count: 14,495
Modeled Residue Count: 1,798
Deposited Residue Count: 1,834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-1	A, B	917	Homo sapiens	Mutation(s): 1 Gene Names: HK1 EC: 2.7.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19367 (Homo sapiens) Explore P19367 Go to UniProtKB: P19367
PHAROS: P19367 GTEx: ENSG00000156515
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G16 Query on G16 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B]	D [auth A], F [auth A], K [auth B], M [auth B]	1,6-di-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₁₂ P₂ RWHOZGRAXYWRNX-VFUOTHLCSA-M		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain M [auth B]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A]	I [auth A], P [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], J [auth B], L [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.273 (Depositor), 0.270 (DCC)
R-Value Work: 0.247 (Depositor), 0.240 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.38	α = 90
b = 120.772	β = 92.8
c = 120.591	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Shen, L.

Honzatko, R.B.

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Structure summary

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Deposit Data

Help and Resources

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Crystal Structure of recombinant human Hexokinase type I mutant D413N with Glucose 1,6-bisphosphate

DETERMINATION of SITE AFFINITY CONSTANTS FOR PRODUCT INHIBITION OF WILD-TYPE AND MUTANT FORMS OF RECOMBINANT HUMAN HEXOKINASE TYPE I

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations