1PMH

Crystal structure of Caldicellulosiruptor saccharolyticus CBM27-1 in complex with mannohexaose

Structural Biology Knowledgebase: 1PMH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.141

Literature

Macromolecules
Sequence Display for 1PMH

Classification: HYDROLASE

Total Structure Weight: 22182.44

Macromolecule Entities
Molecule Chains Length Organism Details
beta-1,4-mannanase X 185 Caldicellulosiruptor saccharolyticus EC#: 3.2.1.78 IUBMB
Fragment: Carbohydrate binding module
Mutation: M17M, F69I, M89M, P104A
Gene Name(s): manA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BMA
Query on BMA

X BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

X ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

X 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

X CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
X L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.141
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 38.28 α = 90.00
b = 45.70 β = 90.00
c = 110.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-11
  • Released Date: 2004-06-22
  • Deposition author(s): Roske, Y., Sunna, A., Heinemann, U.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4