4GM9 | pdb_00004gm9

Crystal structure of human WD repeat domain 5 with compound MM-401

• PDB DOI: https://doi.org/10.2210/pdb4GM9/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-15 Released: 2014-02-19 
• Deposition Author(s): Karatas, H., Townsend, E.C., Chen, Y., Bernard, D., Liu, L., Dou, Y., Lei, M., Wang, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.208 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human WD repeat domain 5 with compound MM-401

Karatas, H., Townsend, E.C., Chen, Y., Bernard, D., Liu, L., Dou, Y., Lei, M., Wang, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.99 kDa 
• Atom Count: 5,406 
• Modeled Residue Count: 629 
• Deposited Residue Count: 636 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MM-401	C [auth E], D [auth F]	5	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0XO	C [auth E], D [auth F]	D-PEPTIDE LINKING	C7 H16 N2 O2		--
ABA	C [auth E], D [auth F]	L-PEPTIDE LINKING	C4 H9 N O2		ALA
PG9	C [auth E], D [auth F]	D-PEPTIDE LINKING	C8 H9 N O2		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000897	C [auth E], D [auth F]	MM-401	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.208 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.904	α = 88.5
b = 47.242	β = 89.5
c = 68.896	γ = 74.53

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Karatas, H., Townsend, E.C., Chen, Y., Bernard, D., Liu, L., Dou, Y., Lei, M., Wang, S.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations