7XS6 | pdb_00007xs6

structure of a membrane-integrated glycosyltransferase with inhibitor

PDB DOI: https://doi.org/10.2210/pdb7XS6/pdb
EM Map EMD-33422: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2022-05-12 Released: 2023-05-17
Deposition Author(s): Wu, Y.N., Zhang, M., Yang, Y.Z., Ding, X.Y., Liu, X.T., Zhang, M.J., Yu, H.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structures and mechanism of chitin synthase and its inhibition by antifungal drug Nikkomycin Z.

Wu, Y., Zhang, M., Yang, Y., Ding, X., Yang, P., Huang, K., Hu, X., Zhang, M., Liu, X., Yu, H.

(2022) Cell Discov 8: 129-129

PubMed: 36473834 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00495-y
Primary Citation of Related Structures:
7XS6, 7XS7

Organizational Affiliation

Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.

Macromolecule Content

Total Structure Weight: 268.65 kDa
Atom Count: 12,440
Modeled Residue Count: 1,458
Deposited Residue Count: 2,262
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin synthase 1	A [auth B], B [auth A]	1,131	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CHS1, YNL192W, N1404 EC: 2.4.1.16 Membrane Entity: Yes
UniProt
Find proteins for P08004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08004 Go to UniProtKB: P08004
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08004
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0V9 Query on 0V9 Download Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A]	Y [auth A], Z [auth A]	(19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate C₃₇ H₇₂ N O₈ P CZOSTDZGCCEZTJ-WMHOIYFHSA-N		Interactions Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain Y [auth A] Focus chain Z [auth A]
BGI (Subject of Investigation/LOI) Query on BGI Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain TA [auth A] MOL2 format, chain X [auth B] MOL2 format, chain TA [auth A] mmCIF format, chain X [auth B] mmCIF format, chain TA [auth A]	TA [auth A], X [auth B]	(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name) C₂₀ H₂₅ N₅ O₁₀ WWJFFVUVFNBJTN-VHDFTHOZSA-N		Interactions Focus chain TA [auth A] Focus chain X [auth B] Interactions & Density Focus chain TA [auth A] Focus chain X [auth B]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain GA [auth A] SDF format, chain G [auth B] SDF format, chain FA [auth A] SDF format, chain F [auth B] SDF format, chain EA [auth A] SDF format, chain E [auth B] SDF format, chain DA [auth A] SDF format, chain D [auth B] SDF format, chain CA [auth A] SDF format, chain C [auth B] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain W [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain G [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain F [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain E [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain D [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain C [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain W [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain G [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain F [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain E [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain D [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain C [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] C [auth B] CA [auth A] D [auth B] AA [auth A], BA [auth A], C [auth B], CA [auth A], D [auth B], DA [auth A], E [auth B], EA [auth A], F [auth B], FA [auth A], G [auth B], GA [auth A], H [auth B], I [auth B], J [auth B], W [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth B] Focus chain CA [auth A] Focus chain D [auth B] Focus chain DA [auth A] Focus chain E [auth B] Focus chain EA [auth A] Focus chain F [auth B] Focus chain FA [auth A] Focus chain G [auth B] Focus chain GA [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth B] Focus chain CA [auth A] Focus chain D [auth B] Focus chain DA [auth A] Focus chain E [auth B] Focus chain EA [auth A] Focus chain F [auth B] Focus chain FA [auth A] Focus chain G [auth B] Focus chain GA [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain W [auth B]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain SA [auth A] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain KA [auth A] SDF format, chain K [auth B] SDF format, chain JA [auth A] SDF format, chain IA [auth A] SDF format, chain HA [auth A] MOL2 format, chain V [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain K [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain HA [auth A] mmCIF format, chain V [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain K [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain HA [auth A]	HA [auth A] IA [auth A] JA [auth A] K [auth B] KA [auth A] HA [auth A], IA [auth A], JA [auth A], K [auth B], KA [auth A], L [auth B], M [auth B], N [auth B], SA [auth A], V [auth B]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain SA [auth A] Focus chain V [auth B] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain SA [auth A] Focus chain V [auth B]
HP6 Query on HP6 Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain RA [auth A] SDF format, chain R [auth B] SDF format, chain QA [auth A] SDF format, chain Q [auth B] SDF format, chain PA [auth A] SDF format, chain P [auth B] SDF format, chain OA [auth A] SDF format, chain O [auth B] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain LA [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth A] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth A] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A]	LA [auth A] MA [auth A] NA [auth A] O [auth B] OA [auth A] LA [auth A], MA [auth A], NA [auth A], O [auth B], OA [auth A], P [auth B], PA [auth A], Q [auth B], QA [auth A], R [auth B], RA [auth A], S [auth B], T [auth B], U [auth B]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain O [auth B] Focus chain OA [auth A] Focus chain P [auth B] Focus chain PA [auth A] Focus chain Q [auth B] Focus chain QA [auth A] Focus chain R [auth B] Focus chain RA [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain O [auth B] Focus chain OA [auth A] Focus chain P [auth B] Focus chain PA [auth A] Focus chain Q [auth B] Focus chain QA [auth A] Focus chain R [auth B] Focus chain RA [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
BGI	BindingDB: 7XS6	IC50: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-05-17
Type: Initial release
Version 1.1: 2024-07-03
Changes: Data collection
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Structure summary
Version 1.3: 2025-06-18
Changes: Data collection