6AAW | pdb_00006aaw

Mdm2 in complex with a D amino Acid Containing Stapled Peptide

PDB DOI: https://doi.org/10.2210/pdb6AAW/pdb

Classification: LIGASE
Organism(s): Homo sapiens, Inovirus M13
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-07-19 Released: 2019-07-24
Deposition Author(s): Brown, C.J., Partridge, A.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.223 (Depositor), 0.229 (DCC)
R-Value Work:
0.184 (Depositor), 0.192 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 3.2 of the entry. See complete history.

Literature

A Model System to Explore Macrocyclic Peptide Structural and Chirality Relationships: Tolerance of helix-breaking residues within the context of a stapled peptide.

Partridge, A.W., Hung, Y.K.K., Juang, Y., Sadruddin, A., Lim, S., Brown, C.J., Ng, S., Thean, D., Ferrer, F., Johannes, C., Yuen, T.Y., Kannan, S., Aronica, P., Tan, Y.S., Mohan, P.R., Verma, C.S., Hichman, J., Chen, S., Wan, H., Lane, D.P., Sawyer, T.K.

To be published.

Macromolecule Content

Total Structure Weight: 15.52 kDa
Atom Count: 878
Modeled Residue Count: 102
Deposited Residue Count: 138
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	122	Homo sapiens	Mutation(s): 0 Gene Names: MDM2 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987 Go to UniProtKB: Q00987
PHAROS: Q00987 GTEx: ENSG00000135679
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00987
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-LEU-THR-PHE-STQ-GLU-TYR-DTR-GLN-LEU-CBA-MK8-SER-ALA-ALA	B	16	Inovirus M13	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0EH Query on 0EH	B	D-PEPTIDE LINKING	C₁₀ H₂₁ N O₂		--
2JH Query on 2JH	B	L-PEPTIDE LINKING	C₇ H₁₃ N O₂		--
DTR Query on DTR	B	D-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₂		--
MK8 Query on MK8	B	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223 (Depositor), 0.229 (DCC)
R-Value Work: 0.184 (Depositor), 0.192 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.946	α = 90
b = 43.378	β = 94.82
c = 34.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PARROT	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Partridge, A.W.

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 2.0: 2023-04-05
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 3.1: 2023-11-29
Changes: Refinement description
Version 3.2: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.