3O8M

Crystal structure of monomeric KlHxk1 in crystal form XI with glucose bound (closed state)

PDB DOI: https://doi.org/10.2210/pdb3O8M/pdb

Classification: TRANSFERASE
Organism(s): Kluyveromyces lactis
Expression System: Kluyveromyces lactis
Mutation(s): No

Deposited: 2010-08-03 Released: 2010-10-13
Deposition Author(s): Kuettner, E.B., Kettner, K., Keim, A., Kriegel, T.M., Strater, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.216
R-Value Work: 0.187
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 54.17 kDa
Atom Count: 4,370
Modelled Residue Count: 472
Deposited Residue Count: 485
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase	A	485	Kluyveromyces lactis	Mutation(s): 0 Gene Names: KLLA0D11352g, RAG5 EC: 2.7.1.1
UniProt
Find proteins for P33284 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P33284 Go to UniProtKB: P33284
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33284
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.216
R-Value Work: 0.187
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.575	α = 90
b = 75.599	β = 90
c = 103.857	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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3O8M

Crystal structure of monomeric KlHxk1 in crystal form XI with glucose bound (closed state)

Entity ID: 1

UniProt

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)