3L3C

Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history



Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN AA,
D [auth B],
G [auth C],
J [auth D]
90Homo sapiensMutation(s): 0 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
GTEx:  ENSG00000077312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')B [auth E],
E [auth F],
H [auth G],
K [auth H]
13N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
GLMS RIBOZYMEC [auth P],
F [auth Q],
I [auth R],
L [auth S]
141N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G6P
Query on G6P

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BA [auth H],
N [auth P],
S [auth Q],
W [auth G]
6-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth R]
CA [auth H]
DA [auth S]
EA [auth S]
FA [auth S]
AA [auth R],
CA [auth H],
DA [auth S],
EA [auth S],
FA [auth S],
M [auth E],
O [auth P],
P,
Q [auth P],
R [auth F],
T [auth Q],
U [auth Q],
V [auth Q],
X [auth G],
Y [auth R],
Z [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.882α = 90
b = 234.947β = 90.55
c = 104.54γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2015-01-21
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Structure summary