4WMW | pdb_00004wmw

The structure of MBP-MCL1 bound to ligand 5 at 1.9A

PDB DOI: https://doi.org/10.2210/pdb4WMW/pdb

Classification: APOPTOSIS
Organism(s): Escherichia coli K-12, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-10-09 Released: 2015-05-06
Deposition Author(s): Clifton, M.C., Dranow, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.214 (Depositor), 0.217 (DCC)
R-Value Work:
0.180 (Depositor), 0.183 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.

Clifton, M.C., Dranow, D.M., Leed, A., Fulroth, B., Fairman, J.W., Abendroth, J., Atkins, K.A., Wallace, E., Fan, D., Xu, G., Ni, Z.J., Daniels, D., Van Drie, J., Wei, G., Burgin, A.B., Golub, T.R., Hubbard, B.K., Serrano-Wu, M.H.

(2015) PLoS One 10: e0125010-e0125010

PubMed: 25909780 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0125010
Primary Citation Related Structures:
4WMR, 4WMS, 4WMT, 4WMU, 4WMV, 4WMW, 4WMX

PubMed Abstract:
Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.

Organizational Affiliation

Beryllium, Bedford, Massachusetts, United States of America.

Macromolecule Content

Total Structure Weight: 58.31 kDa
Atom Count: 4,259
Modeled Residue Count: 514
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MBP-MCL1 chimera protein	A	518	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 3 Gene Names: malE, b4034, JW3994, MCL1, BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for Q07820 (Homo sapiens) Explore Q07820 Go to UniProtKB: Q07820
PHAROS: Q07820 GTEx: ENSG00000143384
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0AEX9 Q07820
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3R6 Query on 3R6 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	2-hydroxy-5-(methylsulfanyl)benzoic acid C₈ H₈ O₃ S DATDARDTUZHWMK-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions 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] Interactions & Density 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]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3R6	BindingDB: 4WMW	IC50: 1.60e+5 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.214 (Depositor), 0.217 (DCC)
R-Value Work: 0.180 (Depositor), 0.183 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.94	α = 90
b = 136.3	β = 90
c = 37.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-05-06

Deposition Author(s):

Clifton, M.C.

Dranow, D.M.

Revision History (Full details and data files)

Version 1.0: 2015-05-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary