4EEM

Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with GLCNAC-BETA1,6-MAN-ALPHA-methyl

PDB DOI: https://doi.org/10.2210/pdb4EEM/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2012-03-28 Released: 2012-07-04
Deposition Author(s): Ramakrishnan, B., Qasba, P.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236
R-Value Work: 0.192
R-Value Observed: 0.194

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: 102.6 kDa
Atom Count: 7,538
Modelled Residue Count: 819
Deposited Residue Count: 861
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,4-galactosyltransferase 1	A, B, C	287	Homo sapiens	Mutation(s): 3 Gene Names: B4GALT1, GGTB2 EC: 2.4.1 (PDB Primary Data), 2.4.1.22 (PDB Primary Data), 2.4.1.90 (PDB Primary Data), 2.4.1.38 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P15291 (Homo sapiens) Explore P15291 Go to UniProtKB: P15291
PHAROS: P15291 GTEx: ENSG00000086062
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15291
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-methyl alpha-D-mannopyranoside	D, E, F	2		N/A	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G72169IP GlyCosmos: G72169IP

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth C]	G [auth A], O [auth B], Y [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	AA [auth C] BA [auth C] CA [auth C] I [auth A] J [auth A] AA [auth C], BA [auth C], CA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain X [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B]	DA [auth C], M [auth A], N [auth A], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain X [auth B] Interactions & Density Focus chain DA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain X [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain Z [auth C] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth C]	H [auth A], P [auth B], Z [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain P [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.351	α = 90
b = 196.386	β = 90
c = 143.755	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-07-04

Deposition Author(s):

Ramakrishnan, B.

Qasba, P.K.

Revision History (Full details and data files)

Version 1.0: 2012-07-04
Type: Initial release
Version 1.1: 2014-03-26
Changes: Database references
Version 1.2: 2017-11-15
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary