1PL6

Human SDH/NADH/inhibitor complex

Structural Biology Knowledgebase: 1PL6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1PL6

Classification: OXIDOREDUCTASE

Total Structure Weight: 158540.09

Macromolecule Entities
Molecule Chains Length Organism Details
Sorbitol dehydrogenase A, B, C, D 356 Homo sapiens EC#: 1.1.1.14 IUBMB
Mutation: M38M, M65M, M107M, M185M, M194M, L238Q, M278M, M309M, M346M
Gene Name(s): SORD Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
572
Query on 572

A, B, C, D 4-[2-(HYDROXYMETHYL)PYRIMIDIN-4-YL]-N,N-DIMETHYLPIPERAZINE- 1-SULFONAMIDE
CP-166572, 2-HYDROXYMETHYL-4-(4-N,N-DIMETHYLAMINOSULFONYL- 1-PIPERAZINO)-PYRIMIDINE (Synonym)
C11 H19 N5 O3 S
XDTHNROWHAAVPJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
572 IC50: 240 - 1000 nM (99) BindingDB

Ki: 154 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.183
  • Space Group: P 62

Unit Cell:

Length (Å) Angle (°)
a = 134.81 α = 90.00
b = 134.81 β = 90.00
c = 225.18 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-07
  • Released Date: 2004-02-17
  • Deposition author(s): Pauly, T.A., Ekstrom, J.L., Beebe, D.A., Chrunyk, B., Cunningham, D., Griffor, M., Kamath, A., Lee, S.E., Madura, R., Mcguire, D., Subashi, T., Wasilko, D., Watts, P., Mylari, B.L., Oates, P.J., Adams, P.D., Rath, V.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values