1GVY

Substrate distorsion by beta-mannanase from Pseudomonas cellulosa

Structural Biology Knowledgebase: 1GVY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.170
  • R-Value Work: 0.144

Literature

Macromolecules
Sequence Display for 1GVY

Classification: HYDROLASE

Total Structure Weight: 44421.19

Macromolecule Entities
Molecule Chains Length Organism Details
MANNAN ENDO-1,4-BETA-MANNOSIDASE A 383 Cellvibrio japonicus EC#: 3.2.1.78 IUBMB
Mutation: E212A
Details: COMPLEX WITH 2,4-DINITROPHENYL 2-DEOXY-2-FLUORO-BETA-MANNOTRIOSIDE
Gene Name(s): manA man26A CJA_2770
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MBF
Query on MBF

A 2-DEOXY-2-FLUORO-BETA-D-MANNOSE
C6 H11 F O5
ZCXUVYAZINUVJD-AIECOIEWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

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

A DINITROPHENYLENE
C6 H4 N2 O4
WDCYWAQPCXBPJA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.170
  • R-Value Work: 0.144
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 93.19 α = 90.00
b = 93.19 β = 90.00
c = 54.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-28
  • Released Date: 2002-09-05
  • Deposition author(s): Ducros, V., Zechel, D.L., Gilbert, H.J., Szabo, L., Withers, S.G., Davies, G.J.

Revision History

  • 2016-12-14
    Type: Source and taxonomy | Details: SOURCE
  • 2016-12-14
    Type: Other | Details: REMARK 100,REMARK 525,MASTER,REMARK 900
  • 2016-12-14
    Type: Non-polymer description | Details: FORMUL
  • 2016-12-14
    Type: Geometry validation | Details: REMARK 500
  • 2016-12-14
    Type: Secondary structure | Details: SHEET
  • 2016-12-14
    Type: Citation | Details: JRNL,REMARK 1
  • 2016-12-14
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2016-12-14
    Type: Biological assembly | Details: REMARK 350
  • 2016-12-14
    Type: Version format compliance | Details: REMARK 4
  • 2016-12-14
    Type: Function and keywords | Details: KEYWDS