3W6N

Crystal structure of human Dlp1 in complex with GMP-PN.Pi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynamin-1-like protein
A, B
364Homo sapiensMutation(s): 0 
Gene Names: DNM1L (DLP1, DRP1)
EC: 3.6.5.5
Find proteins for O00429 (Homo sapiens)
Go to Gene View: DNM1L
Go to UniProtKB:  O00429
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNH
Query on GNH

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A, B
AMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H16 N6 O10 P2
ZGPDMUBRWRJAQQ-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.340α = 90.00
b = 109.020β = 90.00
c = 128.820γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-17 
  • 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
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy