3L43 | pdb_00003l43

Crystal structure of the dynamin 3 GTPase domain bound with GDP

• PDB DOI: https://doi.org/10.2210/pdb3L43/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2009-12-18 Released: 2010-01-19 
• Deposition Author(s): Yang, S., Tempel, W., Tong, Y., Nedyalkova, L., Guan, X., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.269 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the dynamin 3 GTPase domain bound with GDP

Yang, S., Tempel, W., Tong, Y., Nedyalkova, L., Guan, X., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 145.15 kDa 
• Atom Count: 7,535 
• Modeled Residue Count: 965 
• Deposited Residue Count: 1,276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynamin-3	A, B, C, D	319	Homo sapiens	Mutation(s): 1  Gene Names: DNM3, KIAA0820 EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ16 (Homo sapiens) Explore Q9UQ16  Go to UniProtKB:  Q9UQ16
PHAROS:  Q9UQ16 GTEx:  ENSG00000197959

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A], I [auth B], K [auth C], M [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
UNX	F [auth A], G [auth A], H [auth A], J [auth B], L [auth C], N [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.269 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33l43

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.286	α = 90
b = 166.5	β = 109.02
c = 74.985	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Yang, S., Tempel, W., Tong, Y., Nedyalkova, L., Guan, X., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-06-11
  Changes: Refinement description
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2021-10-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description