1ZB5

Recognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40): Crystal structure of the complex of SPP-40 with a peptide Trp-Pro-Trp at 2.45A resolution

• PDB DOI: https://doi.org/10.2210/pdb1ZB5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2005-04-07 Released: 2005-05-10 
• Deposition Author(s): Srivastava, D.B., Ethayathulla, A.S., Kumar, J., Singh, N., Somvanshi, R.K., Sharma, S., Dey, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Recognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40): Crystal structure of the complex of SPP-40 with a peptide Trp-Pro-Trp at 2.45A resolution

Srivastava, D.B., Ethayathulla, A.S., Kumar, J., Singh, N., Somvanshi, R.K., Sharma, S., Dey, S., Kaur, P., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.1 kDa 
• Atom Count: 3,113 
• Modelled Residue Count: 367 
• Deposited Residue Count: 367 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
signal processing protein	A	361	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q29411 (Sus scrofa) Explore Q29411  Go to UniProtKB:  Q29411
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE TRP-PRO-TRP	B, C	3	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.38	α = 90
b = 66.79	β = 90
c = 107.66	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-10 
Deposition Author(s): Srivastava, D.B., Ethayathulla, A.S., Kumar, J., Singh, N., Somvanshi, R.K., Sharma, S., Dey, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2005-05-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary