4H75

Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide

Structural Biology Knowledgebase: 4H75 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 4H75

Classification: GENE REGULATION

Total Structure Weight: 28692.63

Macromolecule Entities
Molecule Chains Length Organism Details
Spindlin-1 A 238 Homo sapiens Fragment: UNP residues 27-262
Gene Name(s): SPIN1 Gene View OCR SPIN
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H3 B 8 Homo sapiens Fragment: H3K4(me3) peptide (UNP residues 2-9)
Gene Name(s): HIST2H3PS2 RP5-998N21.6-001
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NHE
Query on NHE

A 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES (Synonym)
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
B L-PEPTIDE LINKING C9 H21 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.181
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.43 α = 90.00
b = 42.69 β = 90.00
c = 50.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-20
  • Released Date: 2012-10-03
  • Deposition author(s): Yang, N., Wang, W., Wang, Y., Wang, M., Zhao, Q., Rao, Z., Zhu, B., Xu, R.M.

Revision History

  • 2012-11-14
    Type: Citation | Details: Citation update
  • 2012-10-31
    Type: Citation | Details: Citation update