6J9Q

Crystal structure of Trypanosoma brucei gambiense glycerol kinase complex with AMP-PNP.

PDB DOI: https://doi.org/10.2210/pdb6J9Q/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma brucei gambiense
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-24 Released: 2020-01-29
Deposition Author(s): Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269
R-Value Work: 0.191
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Reaction mechanism of the reverse reaction of African human trypanosomes glycerol kinase.

Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

To be published.

Macromolecule Content

Total Structure Weight: 230.84 kDa
Atom Count: 16,007
Modelled Residue Count: 2,052
Deposited Residue Count: 2,072
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	A, B, C, D	518	Trypanosoma brucei gambiense	Mutation(s): 0 Gene Names: gk EC: 2.7.1.30
UniProt
Find proteins for D3KVM3 (Trypanosoma brucei gambiense) Explore D3KVM3 Go to UniProtKB: D3KVM3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3KVM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D]	F [auth A], I [auth B], K [auth C], M [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D]	E [auth A] G [auth B] H [auth B] J [auth C] L [auth D] E [auth A], G [auth B], H [auth B], J [auth C], L [auth D], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth D]