3K5T
Crystal structure of human diamine oxidase in space group C2221
- PDB DOI: https://doi.org/10.2210/pdb3K5T/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): Yes
- Deposited: 2009-10-08 Released: 2010-02-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.290
- R-Value Work: 0.236
- R-Value Observed: 0.239
This is version 2.2 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Diamine oxidase | 731 | Homo sapiens | Mutation(s): 3 Gene Names: ABP1, AOC1, DAO1 EC: 1.4.3.22 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P19801 (Homo sapiens) Explore P19801 Go to UniProtKB: P19801 | |||||
PHAROS: P19801 GTEx: ENSG00000002726 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P19801 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| GOL Query on GOL | G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CU Query on CU | D [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
| CA Query on CA | E [auth A], F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TPQ Query on TPQ | A | L-PEPTIDE LINKING | C9 H9 N O5 |  | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.290
- R-Value Work: 0.236
- R-Value Observed: 0.239
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 94.771 | α = 90 |
| b = 96.954 | β = 90 |
| c = 178.06 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2010-02-09 Deposition Author(s): McGrath, A.P., Guss, J.M.
Revision History (Full details and data files)
- Version 1.0: 2010-02-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2012-03-28
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-10-13
Changes: Database references, Structure summary - Version 2.2: 2023-09-06
Changes: Data collection, Refinement description
