7XS6

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 OPMPDBTMMemProtMD

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 1.1 of the entry. See complete history.

Literature

structure of a membrane-integrated glycosyltransferase with inhibitor

Wu, Y.N., Zhang, M., Yang, Y.Z., Ding, X.Y., Liu, X.T., Zhang, M.J., Yu, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 268.65 kDa
Atom Count: 12,440
Modelled 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 Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [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 TA [auth A] SDF format, chain X [auth B] MOL2 format, chain TA [auth A] MOL2 format, chain X [auth B] mmCIF format, chain TA [auth A] mmCIF format, chain X [auth B]	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 AA [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth B] SDF format, chain CA [auth A] SDF format, chain D [auth B] SDF format, chain DA [auth A] SDF format, chain E [auth B] SDF format, chain EA [auth A] SDF format, chain F [auth B] SDF format, chain FA [auth A] SDF format, chain G [auth B] SDF format, chain GA [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain E [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain C [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain E [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain G [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain W [auth B]	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 HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth B] SDF format, chain KA [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain SA [auth A] SDF format, chain V [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain V [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain V [auth B]	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 LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth A] SDF format, chain P [auth B] SDF format, chain PA [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth A] SDF format, chain R [auth B] SDF format, chain RA [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth A] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	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]