Download MendeleyAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser)
Nakashima, Y., Brewitz, L., Schofield, C.J.To be published.
7YB8
Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser)
- PDB DOI: https://doi.org/10.2210/pdb7YB8/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2022-06-29 Released: 2023-07-05
- Funding Organization(s): Medical Research Council (MRC, United Kingdom)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.248
- R-Value Work: 0.219
- R-Value Observed: 0.221
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Aspartyl/asparaginyl beta-hydroxylase | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor X | 39 | synthetic construct | Mutation(s): 0 EC: 3.4.21.6 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742 | |||||
PHAROS: P00742 GTEx: ENSG00000126218 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00742 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2HG (Subject of Investigation/LOI) Query on 2HG | F [auth A] | (2R)-2-hydroxypentanedioic acid C5 H8 O5 HWXBTNAVRSUOJR-GSVOUGTGSA-N |  | ||
| GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MN Query on MN | E [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.248
- R-Value Work: 0.219
- R-Value Observed: 0.221
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.879 | α = 90 |
| b = 91.063 | β = 90 |
| c = 122.351 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-07-05 Deposition Author(s): Nakashima, Y., Brewitz, L., 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: 2024-11-06
Changes: Structure summary
