4WMX

The structure of MBP-MCL1 bound to ligand 6 at 2.0A

PDB DOI: https://doi.org/10.2210/pdb4WMX/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: 2.00 Å
R-Value Free: 0.217
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 58.44 kDa
Atom Count: 4,387
Modelled Residue Count: 516
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0AEX9Q07820
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3R7 Query on 3R7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	4-ethenyl-2-[(phenylsulfonyl)amino]benzoic acid C₁₅ H₁₃ N O₄ S SWCRJSPSKPQDKL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [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] MOL2 format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [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]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [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]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [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] Interactions & Density Focus chain D [auth A] Focus chain E [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]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3R7	Binding MOAD: 4WMX	Kd: 1.41e+4 (nM) from 1 assay(s)
3R7	BindingDB: 4WMX	IC50: 5000 (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: 2.00 Å
R-Value Free: 0.217
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.56	α = 90
b = 135.87	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

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 1.1: 2015-05-13
Changes: Structure summary
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

Prepare Data

Validate Data

Deposit Data

Help and Resources

4WMX

The structure of MBP-MCL1 bound to ligand 6 at 2.0A

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2