6UAB | pdb_00006uab

Human Mcl-1 in complex with a modified unnatural Bim BH3 peptide

• PDB DOI: https://doi.org/10.2210/pdb6UAB/pdb

• Classification: PEPTIDE BINDING PROTEIN/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-10 Released: 2020-09-16 
• Deposition Author(s): Mandal, T., Grant, R.A., Keating, A.E.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Inhibitor peptides against Mcl-1 containing non-natural amino acids show potent apoptotic response.

Mandal, T., Grant, R.A., Keating, A.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.48 kDa 
• Atom Count: 1,509 
• Modeled Residue Count: 178 
• Deposited Residue Count: 179 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1	A	156	Homo sapiens	Mutation(s): 0  Gene Names: MCL1, BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
PHAROS:  Q07820 GTEx:  ENSG00000143384

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
modified unnatural Bim BH3 peptide	B	23	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
PHAROS:  O43521 GTEx:  ENSG00000153094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADM (Subject of Investigation/LOI)	C [auth B]	ADAMANTANE C10 H16 ORILYTVJVMAKLC-YNFQOJQRSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
NLE	B	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.746	α = 90
b = 56.56	β = 90
c = 99.515	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Mandal, T., Grant, R.A., Keating, A.E.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	--

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary