5M7A

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

PDB DOI: https://doi.org/10.2210/pdb5M7A/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: 1.30 Å
R-Value Free: 0.181
R-Value Work: 0.145
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Blood group synthase AAGlyB in complex with UMP 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: 35.13 kDa
Atom Count: 2,858
Modelled Residue Count: 284
Deposited Residue Count: 298
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	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.181
R-Value Work: 0.145
R-Value Observed: 0.147
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.853	α = 90
b = 149.684	β = 90
c = 79.835	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	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 2.0: 2024-01-17
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5M7A

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

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

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)