3EE5

Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol

PDB DOI: https://doi.org/10.2210/pdb3EE5/pdb

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

Deposited: 2008-09-04 Released: 2009-01-06
Deposition Author(s): Ramakrishnan, B., Qasba, P.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240
R-Value Work: 0.206
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 103.89 kDa
Atom Count: 7,469
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: 2.4.1.38
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-(1-3)-beta-D-galactopyranose	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: G33476GF GlyCosmos: G33476GF GlyGen: G33476GF

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDH Query on UDH Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain Q [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B]	EA [auth C], G [auth A], Q [auth B]	6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE C₁₅ H₂₇ N₃ O₁₂ P₂ MLWJBKPFDKRHBM-FMKGYKFTSA-N		Interactions Focus chain EA [auth C] Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain EA [auth C] Focus chain G [auth A] Focus chain Q [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain IA [auth C] MOL2 format, chain IA [auth C]	IA [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Interactions & Density Focus chain IA [auth C]
2NA Query on 2NA Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain H [auth A] SDF format, chain R [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B]	FA [auth C], H [auth A], R [auth B]	naphthalen-2-ylmethanol C₁₁ H₁₀ O MFGWMAAZYZSWMY-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain H [auth A] Focus chain R [auth B] Interactions & Density Focus chain FA [auth C] Focus chain H [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain J [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain J [auth A]	AA [auth B] BA [auth B] CA [auth B] I [auth A] J [auth A] AA [auth B], BA [auth B], CA [auth B], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	GA [auth C] O [auth A] P [auth A] S [auth B] T [auth B] GA [auth C], O [auth A], P [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain GA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain HA [auth C] MOL2 format, chain HA [auth C]	HA [auth C]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Interactions & Density Focus chain HA [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain LA [auth C] SDF format, chain N [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A]	DA [auth B], LA [auth C], N [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain LA [auth C] Focus chain N [auth A] Interactions & Density Focus chain DA [auth B] Focus chain LA [auth C] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240
R-Value Work: 0.206
R-Value Observed: 0.206
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.127	α = 90
b = 195.742	β = 90
c = 143.801	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MERLOT	phasing
CNS	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: 2009-01-06

Deposition Author(s):

Ramakrishnan, B.

Qasba, P.K.

Revision History (Full details and data files)

Version 1.0: 2009-01-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
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: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2023-08-30
Changes: Data collection, Refinement description