3HM5

SANT domain of human DNA methyltransferase 1 associated protein 1

• PDB DOI: https://doi.org/10.2210/pdb3HM5/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-28 Released: 2009-06-16 
• Deposition Author(s): Dombrovski, L., Tempel, W., Amaya, M.F., Tong, Y., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Park, H., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.275 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

SANT domain of human DNA methyltransferase 1 associated protein 1

Dombrovski, L., Tempel, W., Amaya, M.F., Tong, Y., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Park, H., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.26 kDa 
• Atom Count: 687 
• Modelled Residue Count: 74 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA methyltransferase 1-associated protein 1	A	93	Homo sapiens	Mutation(s): 0  Gene Names: DMAP1, KIAA1425
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF5 (Homo sapiens) Explore Q9NPF5  Go to UniProtKB:  Q9NPF5
PHAROS:  Q9NPF5 GTEx:  ENSG00000178028

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.275 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.523	α = 90
b = 36.523	β = 90
c = 230.506	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Dombrovski, L., Tempel, W., Amaya, M.F., Tong, Y., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Park, H., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations