6GR2 | pdb_00006gr2

Structure of human galactokinase in complex with galactose and ADP

PDB DOI: https://doi.org/10.2210/pdb6GR2/pdb

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

Deposited: 2018-06-08 Released: 2019-06-19
Deposition Author(s): Bezerra, G.A., Mackinnon, S., Williams, E., Zhang, M., Arrowsmith, C., Edwards, A., Bountra, C., Lai, K., Yue, W.W., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.221 (Depositor), 0.223 (DCC)
R-Value Observed:
0.223 (Depositor)

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 in complex with galactose and ADP

Bezerra, G.A., Mackinnon, S., Williams, E., Zhang, M., Arrowsmith, C., Edwards, A., Bountra, C., Lai, K., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 350.16 kDa
Atom Count: 22,955
Modeled Residue Count: 3,066
Deposited Residue Count: 3,192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactokinase	A, B, C, D, E A, B, C, D, E, F, G, H	399	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] SDF format, chain S [auth D] MOL2 format, chain BA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain S [auth D] mmCIF format, chain BA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain S [auth D]	BA [auth H] J [auth A] L [auth B] P [auth C] S [auth D] BA [auth H], J [auth A], L [auth B], P [auth C], S [auth D], U [auth E], W [auth F], Z [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G]
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain Y [auth G] SDF format, chain R [auth D] MOL2 format, chain AA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain R [auth D] mmCIF format, chain AA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain R [auth D]	AA [auth H] I [auth A] K [auth B] O [auth C] R [auth D] AA [auth H], I [auth A], K [auth B], O [auth C], R [auth D], T [auth E], V [auth F], Y [auth G]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain AA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain Y [auth G]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth F]	CA [auth H], M [auth B], N [auth B], Q [auth C], X [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain X [auth F] Interactions & Density Focus chain CA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.221 (Depositor), 0.223 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.217	α = 113.85
b = 110.32	β = 102.26
c = 118.234	γ = 101.29

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106169/ZZ14/Z

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary