4DB1 | pdb_00004db1

Cardiac human myosin S1dC, beta isoform complexed with Mn-AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb4DB1/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2012-01-13 Released: 2012-01-25 
• Deposition Author(s): Klenchin, V.A., Deacon, J.C., Combs, A.C., Leinwand, L.A., Rayment, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Cardiac human myosin S1dC, beta isoform complexed with Mn-AMPPNP

Klenchin, V.A., Deacon, J.C., Combs, A.C., Leinwand, L.A., Rayment, I.

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.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 179.33 kDa 
• Atom Count: 11,340 
• Modeled Residue Count: 1,434 
• Deposited Residue Count: 1,566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin-7	A, B	783	Homo sapiens	Mutation(s): 0  Gene Names: MYH7, MYHCB
UniProt & NIH Common Fund Data Resources
Find proteins for P12883 (Homo sapiens) Explore P12883  Go to UniProtKB:  P12883
PHAROS:  P12883 GTEx:  ENSG00000092054

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN	D [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.206	α = 90
b = 94.31	β = 112.29
c = 110.894	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Klenchin, V.A., Deacon, J.C., Combs, A.C., Leinwand, L.A., Rayment, I.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description