6M5X | pdb_00006m5x

A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to inhibitor heptelidic acid

PDB DOI: https://doi.org/10.2210/pdb6M5X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trichoderma virens Gv29-8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-12 Released: 2020-12-30
Deposition Author(s): Yan, Y., Zang, X., Cooper, S.J., Lin, H., Zhou, J., Tang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.193 (Depositor), 0.195 (DCC)
R-Value Work:
0.150 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance

Yan, Y., Zang, X., Cooper, S.J., Lin, H., Zhou, J., Tang, Y.

(2020) Chem Sci 11: 9554-9562

DOI: https://doi.org/10.1039/D0SC03805A

Macromolecule Content

Total Structure Weight: 149.43 kDa
Atom Count: 11,160
Modeled Residue Count: 1,335
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth O], B [auth R], C [auth P], D [auth Q]	334	Trichoderma virens Gv29-8	Mutation(s): 0 Gene Names: TRIVIDRAFT_217322 EC: 1.2.1.12
UniProt
Find proteins for G9NDK9 (Hypocrea virens (strain Gv29-8 / FGSC 10586)) Explore G9NDK9 Go to UniProtKB: G9NDK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G9NDK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain HA [auth P] SDF format, chain M [auth O] SDF format, chain RA [auth Q] SDF format, chain Y [auth R] MOL2 format, chain HA [auth P] MOL2 format, chain M [auth O] MOL2 format, chain RA [auth Q] MOL2 format, chain Y [auth R] mmCIF format, chain HA [auth P] mmCIF format, chain M [auth O] mmCIF format, chain RA [auth Q] mmCIF format, chain Y [auth R]	HA [auth P], M [auth O], RA [auth Q], Y [auth R]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain HA [auth P] Focus chain M [auth O] Focus chain RA [auth Q] Focus chain Y [auth R] Interactions & Density Focus chain HA [auth P] Focus chain M [auth O] Focus chain RA [auth Q] Focus chain Y [auth R]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth R] MOL2 format, chain X [auth R] mmCIF format, chain X [auth R]	X [auth R]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth R] Interactions & Density Focus chain X [auth R]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth P] SDF format, chain JA [auth P] SDF format, chain N [auth O] SDF format, chain SA [auth Q] SDF format, chain Z [auth R] MOL2 format, chain IA [auth P] MOL2 format, chain JA [auth P] MOL2 format, chain N [auth O] MOL2 format, chain SA [auth Q] MOL2 format, chain Z [auth R] mmCIF format, chain IA [auth P] mmCIF format, chain JA [auth P] mmCIF format, chain N [auth O] mmCIF format, chain SA [auth Q] mmCIF format, chain Z [auth R]	IA [auth P], JA [auth P], N [auth O], SA [auth Q], Z [auth R]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain IA [auth P] Focus chain JA [auth P] Focus chain N [auth O] Focus chain SA [auth Q] Focus chain Z [auth R] Interactions & Density Focus chain IA [auth P] Focus chain JA [auth P] Focus chain N [auth O] Focus chain SA [auth Q] Focus chain Z [auth R]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain GA [auth P] SDF format, chain L [auth O] SDF format, chain OA [auth Q] SDF format, chain PA [auth Q] SDF format, chain QA [auth Q] SDF format, chain W [auth R] MOL2 format, chain GA [auth P] MOL2 format, chain L [auth O] MOL2 format, chain OA [auth Q] MOL2 format, chain PA [auth Q] MOL2 format, chain QA [auth Q] MOL2 format, chain W [auth R] mmCIF format, chain GA [auth P] mmCIF format, chain L [auth O] mmCIF format, chain OA [auth Q] mmCIF format, chain PA [auth Q] mmCIF format, chain QA [auth Q] mmCIF format, chain W [auth R]	GA [auth P] L [auth O] OA [auth Q] PA [auth Q] QA [auth Q] GA [auth P], L [auth O], OA [auth Q], PA [auth Q], QA [auth Q], W [auth R]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth P] Focus chain L [auth O] Focus chain OA [auth Q] Focus chain PA [auth Q] Focus chain QA [auth Q] Focus chain W [auth R] Interactions & Density Focus chain GA [auth P] Focus chain L [auth O] Focus chain OA [auth Q] Focus chain PA [auth Q] Focus chain QA [auth Q] Focus chain W [auth R]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth P] SDF format, chain BA [auth P] SDF format, chain CA [auth P] SDF format, chain DA [auth P] SDF format, chain E [auth O] SDF format, chain EA [auth P] SDF format, chain F [auth O] SDF format, chain FA [auth P] SDF format, chain G [auth O] SDF format, chain H [auth O] SDF format, chain I [auth O] SDF format, chain J [auth O] SDF format, chain K [auth O] SDF format, chain KA [auth Q] SDF format, chain LA [auth Q] SDF format, chain MA [auth Q] SDF format, chain NA [auth Q] SDF format, chain O [auth R] SDF format, chain P [auth R] SDF format, chain Q [auth R] SDF format, chain R SDF format, chain S [auth R] SDF format, chain T [auth R] SDF format, chain U [auth R] SDF format, chain V [auth R] MOL2 format, chain AA [auth P] MOL2 format, chain BA [auth P] MOL2 format, chain CA [auth P] MOL2 format, chain DA [auth P] MOL2 format, chain E [auth O] MOL2 format, chain EA [auth P] MOL2 format, chain F [auth O] MOL2 format, chain FA [auth P] MOL2 format, chain G [auth O] MOL2 format, chain H [auth O] MOL2 format, chain I [auth O] MOL2 format, chain J [auth O] MOL2 format, chain K [auth O] MOL2 format, chain KA [auth Q] MOL2 format, chain LA [auth Q] MOL2 format, chain MA [auth Q] MOL2 format, chain NA [auth Q] MOL2 format, chain O [auth R] MOL2 format, chain P [auth R] MOL2 format, chain Q [auth R] MOL2 format, chain R MOL2 format, chain S [auth R] MOL2 format, chain T [auth R] MOL2 format, chain U [auth R] MOL2 format, chain V [auth R] mmCIF format, chain AA [auth P] mmCIF format, chain BA [auth P] mmCIF format, chain CA [auth P] mmCIF format, chain DA [auth P] mmCIF format, chain E [auth O] mmCIF format, chain EA [auth P] mmCIF format, chain F [auth O] mmCIF format, chain FA [auth P] mmCIF format, chain G [auth O] mmCIF format, chain H [auth O] mmCIF format, chain I [auth O] mmCIF format, chain J [auth O] mmCIF format, chain K [auth O] mmCIF format, chain KA [auth Q] mmCIF format, chain LA [auth Q] mmCIF format, chain MA [auth Q] mmCIF format, chain NA [auth Q] mmCIF format, chain O [auth R] mmCIF format, chain P [auth R] mmCIF format, chain Q [auth R] mmCIF format, chain R mmCIF format, chain S [auth R] mmCIF format, chain T [auth R] mmCIF format, chain U [auth R] mmCIF format, chain V [auth R]	AA [auth P] BA [auth P] CA [auth P] DA [auth P] E [auth O] AA [auth P], BA [auth P], CA [auth P], DA [auth P], E [auth O], EA [auth P], F [auth O], FA [auth P], G [auth O], H [auth O], I [auth O], J [auth O], K [auth O], KA [auth Q], LA [auth Q], MA [auth Q], NA [auth Q], O [auth R], P [auth R], Q [auth R], R, S [auth R], T [auth R], U [auth R], V [auth R]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth P] Focus chain BA [auth P] Focus chain CA [auth P] Focus chain DA [auth P] Focus chain E [auth O] Focus chain EA [auth P] Focus chain F [auth O] Focus chain FA [auth P] Focus chain G [auth O] Focus chain H [auth O] Focus chain I [auth O] Focus chain J [auth O] Focus chain K [auth O] Focus chain KA [auth Q] Focus chain LA [auth Q] Focus chain MA [auth Q] Focus chain NA [auth Q] Focus chain O [auth R] Focus chain P [auth R] Focus chain Q [auth R] Focus chain R Focus chain S [auth R] Focus chain T [auth R] Focus chain U [auth R] Focus chain V [auth R] Interactions & Density Focus chain AA [auth P] Focus chain BA [auth P] Focus chain CA [auth P] Focus chain DA [auth P] Focus chain E [auth O] Focus chain EA [auth P] Focus chain F [auth O] Focus chain FA [auth P] Focus chain G [auth O] Focus chain H [auth O] Focus chain I [auth O] Focus chain J [auth O] Focus chain K [auth O] Focus chain KA [auth Q] Focus chain LA [auth Q] Focus chain MA [auth Q] Focus chain NA [auth Q] Focus chain O [auth R] Focus chain P [auth R] Focus chain Q [auth R] Focus chain R Focus chain S [auth R] Focus chain T [auth R] Focus chain U [auth R] Focus chain V [auth R]