3HIG
Crystal structure of human diamine oxidase in complex with the inhibitor berenil
- PDB DOI: https://doi.org/10.2210/pdb3HIG/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): Yes 
- Deposited: 2009-05-19 Released: 2009-10-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.210 
- R-Value Work: 0.168 
- R-Value Observed: 0.171 
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 |
Amiloride-sensitive amine oxidase | 731 | Homo sapiens | Mutation(s): 1  Gene Names: ABP1 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 | |
BRN Query on BRN | M [auth A], Q [auth B] | BERENIL C14 H15 N7 XNYZHCFCZNMTFY-UHFFFAOYSA-N | |||
GOL Query on GOL | L [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CU Query on CU | I [auth A], N [auth B] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
CA Query on CA | J [auth A], K [auth A], O [auth B], P [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TPQ Query on TPQ | A, B | L-PEPTIDE LINKING | C9 H9 N O5 | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.210 
- R-Value Work: 0.168 
- R-Value Observed: 0.171 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 92.662 | α = 90 |
b = 94.884 | β = 90 |
c = 196.411 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2009-10-20  Deposition Author(s): McGrath, A.P., Guss, J.M.
Revision History (Full details and data files)
- Version 1.0: 2009-10-20
Type: Initial release - Version 1.1: 2011-07-13
Changes: Derived calculations, Non-polymer description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-11-10
Changes: Database references, Structure summary - Version 2.2: 2023-11-01
Changes: Data collection, Refinement description