2WGZ

Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)

PDB DOI: https://doi.org/10.2210/pdb2WGZ/pdb

Classification: TRANSFERASE
Organism(s): Bos taurus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-04-28 Released: 2009-06-16
Deposition Author(s): Jamaluddin, H., Tumbale, P., Ferns, T.A., Thiyagarajan, N., Brew, K., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.206
R-Value Work: 0.169
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 70.59 kDa
Atom Count: 5,487
Modelled Residue Count: 574
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE	A, B	290	Bos taurus	Mutation(s): 0 EC: 2.4.1.151 (PDB Primary Data), 2.4.1.87 (PDB Primary Data)
UniProt
Find proteins for P14769 (Bos taurus) Explore P14769 Go to UniProtKB: P14769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14769
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 E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B]	E [auth A], M [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
147 Query on 147 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	4-nitrophenyl beta-D-galactopyranoside C₁₂ H₁₅ N O₈ IFBHRQDFSNCLOZ-YBXAARCKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NPO Query on NPO Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] N [auth B] F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B]	D [auth A], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.206
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.146	α = 90
b = 94.222	β = 99.05
c = 94.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-06-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary

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2WGZ

Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)