4FOE | pdb_00004foe

Crystal Structure of recombinant human Hexokinase type I with Mannose 6-Phosphate

PDB DOI: https://doi.org/10.2210/pdb4FOE/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.254 (Depositor), 0.248 (DCC)
R-Value Work:
0.244 (Depositor), 0.241 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Inhibitor Sites of Unequal Affinity Linked by Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I

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

To be published.

Macromolecule Content

Total Structure Weight: 207.49 kDa
Atom Count: 14,494
Modeled Residue Count: 1,798
Deposited Residue Count: 1,834
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-1	A, B	917	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M6D Query on M6D Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], K [auth B], M [auth B]	6-O-phosphono-beta-D-mannopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-RWOPYEJCSA-N		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 I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	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 C [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [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 H [auth A] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] 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: 2.70 Å
R-Value Free: 0.254 (Depositor), 0.248 (DCC)
R-Value Work: 0.244 (Depositor), 0.241 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.44	α = 90
b = 122.09	β = 92.65
c = 118.95	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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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: 2018-12-05
Changes: Data collection, Refinement description, Source and taxonomy
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Structure summary

4FOE | pdb_00004foe

Crystal Structure of recombinant human Hexokinase type I with Mannose 6-Phosphate

Literature

Inhibitor Sites of Unequal Affinity Linked by Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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