6Q91

Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide

PDB DOI: https://doi.org/10.2210/pdb6Q91/pdb

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

Deposited: 2018-12-17 Released: 2019-01-23
Deposition Author(s): Mackinnon, S.R., Bezerra, G.A., Zhang, M., Foster, W., Krojer, T., Brandao-Neto, J., Douangamath, A., Arrowsmith, C., Edwards, A., Bountra, C., Brennan, P., Lai, K., Yue, W.W.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.285
R-Value Work: 0.216
R-Value Observed: 0.219

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide

Mackinnon, S.R., Bezerra, G.A., Zhang, M., Foster, W., Krojer, T., Brandao-Neto, J., Douangamath, A., Arrowsmith, C., Edwards, A., Bountra, C., Brennan, P., Lai, K., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 171.4 kDa
Atom Count: 11,516
Modelled Residue Count: 1,536
Deposited Residue Count: 1,568
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactokinase	A, B, C, D	392	Homo sapiens	Mutation(s): 2 Gene Names: GALK1, GALK EC: 2.7.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P51570 (Homo sapiens) Explore P51570 Go to UniProtKB: P51570
PHAROS: P51570 GTEx: ENSG00000108479
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HFK Query on HFK Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	F [auth A], I [auth B], L [auth C]	2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one C₂₀ H₂₂ N₄ O₂ AZBGHUMVHJKFOO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
HR8 Query on HR8 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D]	G [auth A], J [auth B], M [auth C], N [auth D]	5-chloranyl-2-methoxy-~{N}-(2-methylpropyl)benzamide C₁₂ H₁₆ Cl N O₂ GSFUSGKNYXRUQM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth D]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.285
R-Value Work: 0.216
R-Value Observed: 0.219
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.323	α = 90
b = 114.959	β = 100.79
c = 120.918	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092809/Z/10/Z

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-24
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-23
Changes: Structure summary

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Help and Resources

6Q91

Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide

Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)