4XHS | pdb_00004xhs

Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction

• PDB DOI: https://doi.org/10.2210/pdb4XHS/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-01-06 Released: 2016-01-27 
• Deposition Author(s): Jin, T., Huang, M., Jiang, J., Xiao, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction

Jin, T., Huang, M., Jiang, J., Smith, P., Xiao, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.59 kDa 
• Atom Count: 8,321 
• Modeled Residue Count: 906 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12	A, B	480	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, NLRP12, NALP12, PYPAF7, RNO
UniProt & NIH Common Fund Data Resources
Find proteins for P59046 (Homo sapiens) Explore P59046  Go to UniProtKB:  P59046
PHAROS:  P59046 GTEx:  ENSG00000142405

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	E [auth A], F [auth A], I [auth B], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.72	α = 90
b = 103.62	β = 90
c = 186.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Jin, T., Huang, M., Jiang, J., Xiao, T.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary