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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.275 (Depositor), 0.290 (DCC)
R-Value Work:
0.223 (Depositor), 0.230 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPF5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.275 (Depositor), 0.290 (DCC)
R-Value Work: 0.223 (Depositor), 0.230 (DCC)
R-Value Observed: 0.225 (Depositor)

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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