3W6O

Crystal structure of human Dlp1 in complex with GMP-PCP

• PDB DOI: https://doi.org/10.2210/pdb3W6O/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-17 Released: 2014-02-19 
• Deposition Author(s): Kishida, H., Sugio, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Crystal structure of GTPase domain fused with minimal stalks from human dynamin-1-like protein (Dlp1) in complex with several nucleotide analogues

Kishida, H., Sugio, S.

(2013) Curr Top Pept Protein Res 14: 67-77

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.6 kDa 
• Atom Count: 5,942 
• Modelled Residue Count: 678 
• Deposited Residue Count: 728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynamin-1-like protein	A, B	364	Homo sapiens	Mutation(s): 0  Gene Names: DNM1L, DLP1, DRP1 EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for O00429 (Homo sapiens) Explore O00429  Go to UniProtKB:  O00429
PHAROS:  O00429 GTEx:  ENSG00000087470

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	C [auth A], E [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
PG4	G [auth B], H [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CA	I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.24	α = 90
b = 109.07	β = 90
c = 128.3	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Kishida, H., Sugio, S.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-07-23
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description