7YBA | pdb_00007yba

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate

PDB DOI: https://doi.org/10.2210/pdb7YBA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-29 Released: 2023-07-05
Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.202 (Depositor), 0.200 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

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

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate

Nakashima, Y., Brewitz, L., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 49.62 kDa
Atom Count: 3,579
Modeled Residue Count: 428
Deposited Residue Count: 429
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl/asparaginyl beta-hydroxylase	A	429	Homo sapiens	Mutation(s): 0 Gene Names: ASPH EC: 1.14.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q12797 (Homo sapiens) Explore Q12797 Go to UniProtKB: Q12797
PHAROS: Q12797 GTEx: ENSG00000198363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12797
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IO9 (Subject of Investigation/LOI) Query on IO9 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]	(2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid C₅ H₆ O₆ WXSKVKPSMAHCSG-UWTATZPHSA-N		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 B [auth A] MOL2 format, chain B [auth A] mmCIF 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: 1.86 Å
R-Value Free: 0.202 (Depositor), 0.200 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.7	α = 90
b = 70.202	β = 90
c = 172.449	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Schofield, C.J.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.