Macromolecule Content

Total Structure Weight: 417.98 kDa
Atom Count: 25271
Residue Count: 3165
Unique protein chains: 1
Unique nucleic acid chains: 1

7AUD

Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM)

DOI: 10.2210/pdb7AUD/pdb
NDB: 7AUD

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-02 Released: 2020-12-16
Deposition Author(s): Chen, X., Oliver, A.W.
Funding Organization(s): Cancer Research UK, Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.269
R-Value Work: 0.229
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

Literature

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein

Chen, X., Ali, Y., Fisher, C.E.L., Arribas-Bosacoma, R., Rajasekaran, M.B., Williams, G., Walker, S., Roe, S.M., Pearl, L.H., Ward, S.E., Pearl, F.M.G., Oliver, A.W.

(2020) Biorxiv

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bloom syndrome protein,Bloom syndrome protein	A, B, C, D, E, F	563	Homo sapiens	Mutation(s): 0 Gene Names: BLM, RECQ2, RECQL3 EC: 3.6.4.12
Find proteins for P54132 (Homo sapiens) Explore P54132 Go to UniProtKB: P54132
NIH Common Fund Data Resources
PHAROS P54132 GTEx ENSG00000197299
Protein Feature View Expand
Reference Sequence

Find similar nucleic acids by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPTPAPCPCPCPGPAPTPGPTPGP*T)-3')	M, N, O, P, Q, R	15	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [D] SDF format, chain FA [E] SDF format, chain JA [F] SDF format, chain N [A] SDF format, chain S [B] SDF format, chain W [C] MOL2 format, chain BA [D] MOL2 format, chain FA [E] MOL2 format, chain JA [F] MOL2 format, chain N [A] MOL2 format, chain S [B] MOL2 format, chain W [C]	A, B, C, D, E, F	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Ligand Interaction
RY8 Query on RY8 Download Ideal Coordinates CCD File SDF format, chain CA [D] SDF format, chain GA [E] SDF format, chain KA [F] SDF format, chain O [A] SDF format, chain T [B] SDF format, chain X [C] MOL2 format, chain CA [D] MOL2 format, chain GA [E] MOL2 format, chain KA [F] MOL2 format, chain O [A] MOL2 format, chain T [B] MOL2 format, chain X [C]	A, B, C, D, E, F	N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide C₁₉ H₁₉ N₃ O₃ S₂ GGIKQVGRVUTAKR-UHFFFAOYSA-N		Ligand Interaction
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain DA [D] SDF format, chain HA [E] SDF format, chain P [A] SDF format, chain Q [A] SDF format, chain U [B] SDF format, chain Y [C] SDF format, chain Z [C] MOL2 format, chain DA [D] MOL2 format, chain HA [E] MOL2 format, chain P [A] MOL2 format, chain Q [A] MOL2 format, chain U [B] MOL2 format, chain Y [C] MOL2 format, chain Z [C]	A, B, C, D, E	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [D] SDF format, chain EA [E] SDF format, chain IA [F] SDF format, chain M [A] SDF format, chain R [B] SDF format, chain V [C] MOL2 format, chain AA [D] MOL2 format, chain EA [E] MOL2 format, chain IA [F] MOL2 format, chain M [A] MOL2 format, chain R [B] MOL2 format, chain V [C]	A, B, C, D, E, F	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain LA [F] SDF format, chain MA [M] SDF format, chain NA [N] SDF format, chain OA [P] SDF format, chain PA [Q] SDF format, chain QA [Q] MOL2 format, chain LA [F] MOL2 format, chain MA [M] MOL2 format, chain NA [N] MOL2 format, chain OA [P] MOL2 format, chain PA [Q] MOL2 format, chain QA [Q]	F, M, N, P, Q	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.269
R-Value Work: 0.229
R-Value Observed: 0.231
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.916	α = 72.64
b = 111.709	β = 80.18
c = 132.344	γ = 79.22

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-11-02
Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C302/A24386
Wellcome Trust	United Kingdom	110578/Z/15/Z

Revision History

Version 1.0: 2020-12-16
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.