1BG3 | pdb_00001bg3

RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb1BG3/pdb

Classification: HEXOKINASE
Organism(s): Rattus norvegicus
Mutation(s): No

Deposited: 1998-06-04 Released: 1999-06-08
Deposition Author(s): Mulichak, A.M., Garavito, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.251 (Depositor)
R-Value Work:
0.196 (Depositor), 0.195 (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 1.5 of the entry. See complete history.

Literature

The structure of mammalian hexokinase-1.

Mulichak, A.M., Wilson, J.E., Padmanabhan, K., Garavito, R.M.

(1998) Nat Struct Biol 5: 555-560

PubMed: 9665168 Search on PubMed
DOI: https://doi.org/10.1038/811
Primary Citation Related Structures:
1BDG, 1BG3

PubMed Abstract:
We have determined the structures of the glucose-6-phosphate (G6P)-inhibitable 100,000 Mr Type I hexokinase from rat and the G6P-sensitive 50,000 Mr hexokinase from Schistosoma mansoni at a resolution of 2.8 and 2.6 A respectively. The structures define the glucose and G6P binding sites in these enzymes, suggest the mechanisms of intradomain G6P inhibition and activity loss in the Type I hexokinase N-terminal half, and reveal the structure of the membrane targeting motif that integrates the Type I hexokinase into the outer mitochondrial membrane.

Organizational Affiliation

Department of Biochemistry, Michigan State University, East Lansing, USA. mulichak@alecto.bch.msu.edu

Macromolecule Content

Total Structure Weight: 206.89 kDa
Atom Count: 13,962
Modeled Residue Count: 1,804
Deposited Residue Count: 1,836
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEXOKINASE	A, B	918	Rattus norvegicus	Mutation(s): 0 EC: 2.7.1.1
UniProt
Find proteins for P05708 (Rattus norvegicus) Explore P05708 Go to UniProtKB: P05708
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05708
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G6P Query on G6P Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth A], I [auth B], K [auth B]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth A], H [auth B], J [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.251 (Depositor)
R-Value Work: 0.196 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.1	α = 90
b = 77.1	β = 96
c = 137.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1999-06-08

Deposition Author(s):

Mulichak, A.M.

Garavito, R.M.

Revision History (Full details and data files)

Version 1.0: 1999-06-08
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2024-02-07
Changes: Data collection, Database references, Structure summary
Version 1.5: 2024-04-03
Changes: Refinement description