3SWR | pdb_00003swr

Structure of human DNMT1 (601-1600) in complex with Sinefungin

PDB DOI: https://doi.org/10.2210/pdb3SWR/pdb

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

Deposited: 2011-07-14 Released: 2011-08-10
Deposition Author(s): Hashimoto, H., Cheng, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.272 (Depositor), 0.260 (DCC)
R-Value Work:
0.220 (Depositor), 0.210 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of human DNMT1 (residues 600-1600) in complex with Sinefungin

Hashimoto, H., Cheng, X.

To be published.

Macromolecule Content

Total Structure Weight: 116.35 kDa
Atom Count: 7,924
Modeled Residue Count: 965
Deposited Residue Count: 1,002
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 (cytosine-5)-methyltransferase 1	A	1,002	Homo sapiens	Mutation(s): 0 Gene Names: DNMT1, AIM, CXXC9, DNMT EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P26358 (Homo sapiens) Explore P26358 Go to UniProtKB: P26358
PHAROS: P26358 GTEx: ENSG00000130816
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26358
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG Query on SFG 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]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain HA [auth A] SDF format, chain GA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain GA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain GA [auth A]	EA [auth A], FA [auth A], GA [auth A], HA [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain U [auth A] SDF format, chain P [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain U [auth A] MOL2 format, chain P [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain U [auth A] mmCIF format, chain P [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] F [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.272 (Depositor), 0.260 (DCC)
R-Value Work: 0.220 (Depositor), 0.210 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60	α = 90
b = 110.77	β = 90
c = 201.26	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Hashimoto, H.

Cheng, X.

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description