9F3L | pdb_00009f3l

Crystal structure of Kluyveromyces lactis glucokinase mutant H304Q in complex with mannose

PDB DOI: https://doi.org/10.2210/pdb9F3L/pdb

Classification: TRANSFERASE
Organism(s): Kluyveromyces lactis
Expression System: Kluyveromyces
Mutation(s): Yes

Deposited: 2024-04-25 Released: 2025-05-14
Deposition Author(s): Weisse, R.H., Strater, N.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1

Weisse, R.H., Kettner, K., Lilie, H., Funk, L., Roedel, G., Tittmann, K., Strater, N., Kriegel, T.M.

To be published.

Macromolecule Content

Total Structure Weight: 217.91 kDa
Atom Count: 15,399
Modeled Residue Count: 1,920
Deposited Residue Count: 1,924
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase-1	A, B, C, D	481	Kluyveromyces lactis	Mutation(s): 1 Gene Names: GLK1, KLLA0C01155g EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (PDB Primary Data)
UniProt
Find proteins for Q6CUZ3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CUZ3 Go to UniProtKB: Q6CUZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6CUZ3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN (Subject of Investigation/LOI) Query on MAN Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain U [auth D] SDF format, chain E [auth A] SDF format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth C]	E [auth A], I [auth B], N [auth C], U [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain U [auth D]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] F [auth A] G [auth A] H [auth A] J [auth B] AA [auth D], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]