6UAB

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240
R-Value Work: 0.190
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07820
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43521
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADM (Subject of Investigation/LOI) Query on ADM Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	ADAMANTANE C₁₀ H₁₆ ORILYTVJVMAKLC-YNFQOJQRSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
NLE Query on 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
R-Value Work: 0.190
R-Value Observed: 0.195
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release

RCSB PDB Core Operations are 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.