6S24

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3

PDB DOI: https://doi.org/10.2210/pdb6S24/pdb

Classification: TRANSFERASE
Organism(s): Taeniopygia guttata, Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2019-06-20 Released: 2019-12-25
Deposition Author(s): de las Rivas, M., Daniel, E.J.P., Narimatsu, Y., Companon, I., Kato, K., Hermosilla, P., Thureau, A., Ceballos-Laita, L., Coelho, H., Bernado, P., Marcelo, F., Hansen, L., Lostao, A., Corzana, F., Clausen, H., Gerken, T.A., Hurtado-Guerrero, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.237
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 76.04 kDa
Atom Count: 4,756
Modelled Residue Count: 551
Deposited Residue Count: 645
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polypeptide N-acetylgalactosaminyltransferase	A	631	Taeniopygia guttata	Mutation(s): 0 Gene Names: GALNT3 EC: 2.4.1
UniProt
Find proteins for H0ZAB5 (Taeniopygia guttata) Explore H0ZAB5 Go to UniProtKB: H0ZAB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H0ZAB5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO	B [auth F]	14	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
NGA (Subject of Investigation/LOI) Query on NGA Download Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F]	V [auth F]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A]	U [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain W [auth F] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth F] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], W [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth F] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth F]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.237
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.655	α = 90
b = 104.661	β = 90
c = 143.186	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2020-01-22
Changes: Database references
Version 1.2: 2020-03-04
Changes: Data collection, Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary