Download MendeleySynthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase
Brewitz, L., Nakashima, Y., Schofield, C.J.(2021) Chem Sci 12: 1327-1342
6YYX
Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-methyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser)
- PDB DOI: https://doi.org/10.2210/pdb6YYX/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3), synthetic construct
- Mutation(s): Yes
- Deposited: 2020-05-06 Released: 2021-03-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.192
- R-Value Work: 0.162
- R-Value Observed: 0.164
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
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, BAH 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 | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor X | 39 | Homo sapiens | Mutation(s): 4 Gene Names: F10 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 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| Q1Z (Subject of Investigation/LOI) Query on Q1Z | D [auth A] | (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid C6 H8 O5 BJQIUPTURRAODO-GSVOUGTGSA-N |  | ||
| MN (Subject of Investigation/LOI) Query on MN | C [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.192
- R-Value Work: 0.162
- R-Value Observed: 0.164
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.22 | α = 90 |
| b = 86.591 | β = 90 |
| c = 123.265 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| STARANISO | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2021-03-17 Deposition Author(s): Nakashima, Y., Brewitz, L., Schofield, C.J.
Revision History (Full details and data files)
- Version 1.0: 2021-03-17
Type: Initial release - Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description - Version 1.2: 2024-11-06
Changes: Structure summary
