1bg3

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

Method: X-RAY DIFFRACTION D_max: 141.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

HEXOKINASE

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–918	Not recorded	BGC beta-D-glucopyranose × 2 G6P 6-O-phosphono-alpha-D-glucopyranose × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.80 Å R-free 0.251
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–918	Not recorded	BGC beta-D-glucopyranose × 2 G6P 6-O-phosphono-alpha-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.80 Å R-free 0.251

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	HXK1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–918； UniProt 1–918 Author chain B； PDBConstruct 1–918； UniProt 1–918

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bg3
Deposition date deposition_date	1998-06-04
Structure title title	RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE
Keywords keywords	HEXOKINASE, PHOSPHOTRANSFERASE; HEXOKINASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	42.31 Å
Radius of gyration Rg (electron density) rg_electron	41.91 Å
Forward intensity I(0) i0	582102000.00
Molecular weight molecular_weight	196210.0 kDa
Excluded volume excluded_volume	244720 Å³
Envelope volume envelope_volume	319660 Å³
Hydration-shell volume shell_volume	62995 Å³
Envelope diameter envelope_diameter	142.3 Å
Shell Rg shell_rg	48.05 Å
Envelope Rg envelope_rg	41.05 Å
Shape Rg shape_rg	41.92 Å
Total Rg total_rg	42.17 Å
Total atoms total_atoms	13728
Residues n_residues	1804
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	141.2 Å
Rg (real space) rg_real	42.26 Å
Rg uncertainty (real space) rg_real_error	1.61 Å
I(0) (real space) i0_real	5.8210e+08
I(0) uncertainty (real space) i0_real_error	9.8840e+06
Rg (reciprocal space) rg_reciprocal	42.31 Å
I(0) (reciprocal space) i0_reciprocal	582100000.0000
Solution quality estimate total_estimate	0.8216
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	53.5 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.445
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52390000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HEXOKINASE
Molecular weight formula_weight	102545.2 kDa
EC 编号 ec_number	2.7.1.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13962

MIAAQLLAYYFTELKDDQVKKIDKYLYAMRLSDEILIDILTRFKKEMKNGLSRDYNPTASVKMLPTFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNHEKNQNVSMESEIYDTPENIVHGSGTQLFDHVADCLGDFMEKKKIKDKKLPVGFTFSFPCRQSKIDEAVLITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGTMMTCGYDDQQCEVGLIIGTGTNACYMEELRHIDLVEGDEGRMCINTEWGAFGDDGSLEDIRTEFDRELDRGSLNPGKQLFEKMVSGMYMGELVRLILVKMAKEGLLFEGRITPELLTRGKFNTSDVSAIEKDKEGIQNAKEILTRLGVEPSDVDCVSVQHICTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGSLYKMHPQYSRRFHKTLRRLVPDSDVRFLLSESGTGKGAAMVTAVAYRLAEQHRQIEETLAHFRLSKQTLMEVKKRLRTEMEMGLRKETNSKATVKMLPSFVRSIPDGTEHGDFLALDLGGTNFRVLLVKIRSGKKRTVEMHNKIYSIPLEIMQGTGDELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCHQTNLDCGILISWTKGFKATDCEGHDVASLLRDAVKRREEFDLDVVAVVNDTVGTMMTCAYEEPTCEIGLIVGTGTNACYMEEMKNVEMVEGNQGQMCINMEWGAFGDNGCLDDIRTDFDKVVDEYSLNSGKQRFEKMISGMYLGEIVRNILIDFTKKGFLFRGQISEPLKTRGIFETKFLSQIESDRLALLQVRAILQQLGLNSTCDDSILVKTVCGVVSKRAAQLCGAGMAAVVEKIRENRGLDHLNVTVGVDGTLYKLHPHFSRIMHQTVKELSPKCTVSFLLSEDGSGKGAALITAVGVRLRGDPSIA

Entity 2 Entity 2 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	6-O-phosphono-alpha-D-glucopyranose
Molecular weight formula_weight	260.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1bg3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3a4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3b3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

Domain ID domain_id	d1bg3b4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.3 — Hexokinase

CATH v4.4 (8 domains)

Domain ID domain_id	1bg3A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1bg3A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1bg3A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1bg3A04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1bg3B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1bg3B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1bg3B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1bg3B04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	132.100 Å
Unit-cell length b length_b	77.100 Å
Unit-cell length c length_c	137.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2510

fit	/app/data/saxs_computation/bg/1bg3/1bg3.fit
pddf	/app/data/pr_computation/bg/1bg3/1bg3.pr.out
profile	/app/data/saxs_computation/bg/1bg3/1bg3.dat