5M7C

Blood group synthase AAGlyB in complex with UDP and cryoprotected with PEG 3350

PDB DOI: https://doi.org/10.2210/pdb5M7C/pdb

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

Deposited: 2016-10-27 Released: 2017-11-29
Deposition Author(s): Rocha, J., Royant, A.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.180
R-Value Work: 0.151
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Blood group synthase AAGlyB in complex with UDP and cryoprotected with PEG 3350

Rocha, J., Batot, G.O., Palcic, M.M., Breton, C., Royant, A.

To be published.

Macromolecule Content

Total Structure Weight: 70.63 kDa
Atom Count: 5,452
Modelled Residue Count: 586
Deposited Residue Count: 596
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, B	298	Homo sapiens	Mutation(s): 2 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	G [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.180
R-Value Work: 0.151
R-Value Observed: 0.152
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.73	α = 90
b = 77.768	β = 109.19
c = 79.995	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-11-29

Deposition Author(s):

Rocha, J.

Royant, A.

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-13-BSV8-0011-02

Revision History (Full details and data files)

Version 1.0: 2017-11-29
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5M7C

Blood group synthase AAGlyB in complex with UDP and cryoprotected with PEG 3350

Blood group synthase AAGlyB in complex with UDP and cryoprotected with PEG 3350

Entity ID: 1

UniProt & NIH Common Fund Data Resources

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)