2NZ4
Structural investigation of the GlmS ribozyme bound to its catalytic cofactor
- PDB DOI: https://doi.org/10.2210/pdb2NZ4/pdb
- NAKB: 2NZ4
- Classification: STRUCTURAL PROTEIN/RNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21
- Mutation(s): Yes 
- Deposited: 2006-11-22 Released: 2007-01-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.269 
- R-Value Work: 0.222 
- R-Value Observed: 0.224 
This is version 1.5 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
U1 Small Nuclear Ribonucleoprotein A | I [auth A], J [auth B], K [auth C], L [auth D] | 94 | Homo sapiens | Mutation(s): 2  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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P09012 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
substrate strand RNA 13-mer | A [auth E], C [auth F], E [auth G], G [auth H] | 13 | N/A | ||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
GlmS ribozyme | B [auth P], D [auth Q], F [auth R], H [auth S] | 141 | N/A | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GLP Query on GLP | BA [auth H], M [auth P], R [auth F], W [auth G] | 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C6 H14 N O8 P XHMJOUIAFHJHBW-UKFBFLRUSA-N | |||
MG Query on MG | AA [auth R] CA [auth H] DA [auth H] EA [auth S] FA [auth S] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.269 
- R-Value Work: 0.222 
- R-Value Observed: 0.224 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 48.127 | α = 90 |
b = 234.157 | β = 90.65 |
c = 105.003 | γ = 90 |
Software Name | Purpose |
---|---|
CBASS | data collection |
SHARP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2007-01-16  Deposition Author(s): Cochrane, J.C.
Revision History (Full details and data files)
- Version 1.0: 2007-01-16
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2021-10-20
Changes: Database references, Structure summary - Version 1.5: 2023-12-27
Changes: Data collection, Refinement description