4Y63

AAGlyB in complex with amino-acid analogues

PDB DOI: https://doi.org/10.2210/pdb4Y63/pdb

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

Deposited: 2015-02-12 Released: 2015-09-16
Deposition Author(s): Wang, S., Cuesta-Seijo, J.A., Striebeck, A., Lafont, D., Palcic, M.M., Vidal, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.183
R-Value Work: 0.159
R-Value Observed: 0.160

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates?

Wang, S., Cuesta-Seijo, J.A., Striebeck, A., Lafont, D., Palcic, M.M., Vidal, S.

(2015) Chempluschem 80: 1525-1532

DOI: https://doi.org/10.1002/cplu.201500282

Macromolecule Content

Total Structure Weight: 41.78 kDa
Atom Count: 2,765
Modelled Residue Count: 282
Deposited Residue Count: 354
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histo-blood group ABO system transferase	A	354	Homo sapiens	Mutation(s): 1 Gene Names: ABO EC: 2.4.1.40 (PDB Primary Data), 2.4.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens) Explore P16442 Go to UniProtKB: P16442
PHAROS: P16442
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16442
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BHE Query on BHE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside C₂₀ H₃₈ O₁₀ GTTDTLMUWQMDNA-ARNYJBIMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
48O Query on 48O Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5'-deoxy-5'-{[(2S)-2-(triaza-1,2-dien-2-ium-1-yl)propanoyl]amino}uridine C₁₂ H₁₇ N₆ O₆ BMVPLHCMGOWMGY-DANLAGSESA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.183
R-Value Work: 0.159
R-Value Observed: 0.160
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.84	α = 90
b = 149.15	β = 90
c = 80.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-16
Type: Initial release
Version 1.1: 2017-08-30
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description

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4Y63

AAGlyB in complex with amino-acid analogues

Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates?

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)