7YRO

Crystal structure of mango fucosyltransferase 13

PDB DOI: https://doi.org/10.2210/pdb7YRO/pdb

Classification: TRANSFERASE
Organism(s): Mangifera indica
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-08-10 Released: 2023-08-16
Deposition Author(s): Okada, T., Teramoto, T., Ihara, H., Ikeda, Y., Kakuta, Y.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of mango alpha1,3/alpha1,4-fucosyltransferase elucidates unique elements strictly regulating its type I-dominant acceptor preference

Okada, T., Teramoto, T., Ihara, H., Ikeda, Y., Kakuta, Y.

To be published.

Macromolecule Content

Total Structure Weight: 374.09 kDa
Atom Count: 21,872
Modelled Residue Count: 2,681
Deposited Residue Count: 3,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucosyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	410	Mangifera indica	Mutation(s): 0 Gene Names: FUT13 EC: 2.4.1
UniProt
Find proteins for A0A292GKJ7 (Mangifera indica) Explore A0A292GKJ7 Go to UniProtKB: A0A292GKJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A292GKJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain M [auth B] SDF format, chain PA [auth F] SDF format, chain R [auth C] SDF format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth C] MOL2 format, chain AA [auth D]	AA [auth D], GA [auth E], M [auth B], PA [auth F], R [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain M [auth B] Focus chain PA [auth F] Focus chain R [auth C] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth E] Focus chain M [auth B] Focus chain PA [auth F] Focus chain R [auth C]
PPV (Subject of Investigation/LOI) Query on PPV Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain L [auth B] SDF format, chain LA [auth F] SDF format, chain Q [auth C] SDF format, chain RA [auth G] SDF format, chain UA [auth H] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain RA [auth G] MOL2 format, chain UA [auth H] MOL2 format, chain Z [auth D]	FA [auth E] L [auth B] LA [auth F] Q [auth C] RA [auth G] FA [auth E], L [auth B], LA [auth F], Q [auth C], RA [auth G], UA [auth H], Z [auth D]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain L [auth B] Focus chain LA [auth F] Focus chain Q [auth C] Focus chain RA [auth G] Focus chain UA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain L [auth B] Focus chain LA [auth F] Focus chain Q [auth C] Focus chain RA [auth G] Focus chain UA [auth H] Focus chain Z [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain I [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain SA [auth G] SDF format, chain T [auth C] SDF format, chain VA [auth H] SDF format, chain W [auth C] SDF format, chain Y [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain OA [auth F] SDF format, chain U [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] HA [auth E] BA [auth D], CA [auth D], DA [auth D], EA [auth D], HA [auth E], I [auth A], JA [auth E], KA [auth E], MA [auth F], N [auth B], NA [auth F], O [auth B], OA [auth F], S [auth C], SA [auth G], T [auth C], U [auth C], VA [auth H], W [auth C], X [auth C], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain S [auth C] Focus chain SA [auth G] Focus chain T [auth C] Focus chain U [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain S [auth C] Focus chain SA [auth G] Focus chain T [auth C] Focus chain U [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
ACY (Subject of Investigation/LOI) Query on ACY Download Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain P [auth B] SDF format, chain QA [auth F] SDF format, chain TA [auth G] SDF format, chain V [auth C] SDF format, chain J [auth A] SDF format, chain WA [auth H] MOL2 format, chain IA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain TA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain J [auth A] MOL2 format, chain WA [auth H]	IA [auth E] J [auth A] P [auth B] QA [auth F] TA [auth G] IA [auth E], J [auth A], P [auth B], QA [auth F], TA [auth G], V [auth C], WA [auth H]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain IA [auth E] Focus chain J [auth A] Focus chain P [auth B] Focus chain QA [auth F] Focus chain TA [auth G] Focus chain V [auth C] Focus chain WA [auth H] Interactions & Density Focus chain IA [auth E] Focus chain J [auth A] Focus chain P [auth B] Focus chain QA [auth F] Focus chain TA [auth G] Focus chain V [auth C] Focus chain WA [auth H]